Double peak-induced distance error in short-time-Fourier-transform-Brillouin optical time domain reflectometers event detection and the recovery method.

PubMed

Yu, Yifei; Luo, Linqing; Li, Bo; Guo, Linfeng; Yan, Jize; Soga, Kenichi

2015-10-01

The measured distance error caused by double peaks in the BOTDRs (Brillouin optical time domain reflectometers) system is a kind of Brillouin scattering spectrum (BSS) deformation, discussed and simulated for the first time in the paper, to the best of the authors' knowledge. Double peak, as a kind of Brillouin spectrum deformation, is important in the enhancement of spatial resolution, measurement accuracy, and crack detection. Due to the variances of the peak powers of the BSS along the fiber, the measured starting point of a step-shape frequency transition region is shifted and results in distance errors. Zero-padded short-time-Fourier-transform (STFT) can restore the transition-induced double peaks in the asymmetric and deformed BSS, thus offering more accurate and quicker measurements than the conventional Lorentz-fitting method. The recovering method based on the double-peak detection and corresponding BSS deformation can be applied to calculate the real starting point, which can improve the distance accuracy of the STFT-based BOTDR system.

Portable Infrared Reflectometer Designed and Manufactured for Evaluating Emittance in the Laboratory or in the Field

NASA Technical Reports Server (NTRS)

Jaworske, Donald A.

2000-01-01

The optical properties of materials play a key role in spacecraft thermal control. In space, radiant heat transfer is the only mode of heat transfer that can reject heat from a spacecraft. One of the key properties for defining radiant heat transfer is emittance, a measure of how efficiently a surface can reject heat in comparison to a perfect black body emitter. Heat rejection occurs in the infrared region of the spectrum, nominally in the range of 2 to 25 mm. To calculate emittance, one obtains the reflectance over this spectral range, calculates spectral absorptance by difference, and then uses Kirchhoff s Law and the Stefan-Boltzmann equation to calculate emittance. A new portable infrared reflectometer, the SOC 400t, was designed and manufactured to evaluate the emittance of surfaces and coatings in the laboratory or in the field. It was developed by Surface Optics Corporation under a contract with the NASA Glenn Research Center at Lewis Field to replace the Center s aging Gier-Dunkle DB-100 infrared reflectometer. The specifications for the new instrument include a wavelength range of 2 to 25 mm; reflectance repeatability of +/-1 percent; self-calibrating, near-normal spectral reflectance measurements; a full scan measurement time of 3.5 min, a sample size of 1.27 cm (0.5 in.); a spectral resolution selectable from 4, 8, 16, or 32/cm; and optical property characterization utilizing an automatic integration to calculate total emittance in a selectable temperature range.

Reflectometer design using nonimaging optics

NASA Astrophysics Data System (ADS)

Snail, Keith A.

1987-12-01

A new type of two-stage reflectometer is proposed for the measurement of directional hemispherical reflectance. The proposed reflectometer consists of a primary collecting mirror coupled to a secondary mirror chosen to eliminate the Fresnel variation of the detector (or source) response. The secondary mirror shape needed is an inverted nonimaging compound parabolic concentrator (CPC). For direct mode operation, the detector is placed at the larger CPC aperture. Ray tracing of a CPC/ellipsoid reflectometer indicates that the throughput is high and isotropic. Design trade-offs and two-stage reflectometers employing a hemisphere and dual paraboloid primary are also discussed.

Reflectometer design using nonimaging optics.

PubMed

Snail, K A

1987-12-15

A new type of two-stage reflectometer is proposed for the measurement of directional hemispherical reflectance. The proposed reflectometer consists of a primary collecting mirror coupled to a secondary mirror chosen to eliminate the Fresnel variation of the detector (or source) response. The secondary mirror shape needed is an inverted nonimaging compound parabolic concentrator (CPC). For direct mode operation, the detector is placed at the larger CPC aperture. Ray tracing of a CPC/ellipsoid reflectometer indicates that the throughput is high and isotropic. Design trade-offs and two-stage reflectometers employing a hemisphere and dual paraboloid primary are also discussed.

High-resolution differential mode delay measurement for a multimode optical fiber using a modified optical frequency domain reflectometer.

PubMed

Ahn, T-J; Kim, D

2005-10-03

A novel differential mode delay (DMD) measurement technique for a multimode optical fiber based on optical frequency domain reflectometry (OFDR) has been proposed. We have obtained a high-resolution DMD value of 0.054 ps/m for a commercial multimode optical fiber with length of 50 m by using a modified OFDR in a Mach-Zehnder interferometer structure with a tunable external cavity laser and a Mach-Zehnder interferometer instead of Michelson interferometer. We have also compared the OFDR measurement results with those obtained using a traditional time-domain measurement method. DMD resolution with our proposed OFDR technique is more than an order of magnitude better than a result obtainable with a conventional time-domain method.

Possible applications of time domain reflectometry in planetary exploration missions

NASA Technical Reports Server (NTRS)

Heckendorn, S.

1982-01-01

The use of a time domain reflectometer (TDR) for planetary exploration is considered. Determination of the apparent dielectric constant and hence, the volumetric water content of frozen and unfrozen soils using the TDR is described. Earth-based tests were performed on a New York state sandy soil and a Wyoming Bentonite. Use of both a cylindrical coaxial transmission line and a parallel transmission line as probes was evaluated. The water content of the soils was varied and the apparent dielectric constant measured in both frozen and unfrozen states. Advantages and disadvantages of the technique are discussed.

Application of Time Domain Reflectometers in Urban Settings ...

EPA Pesticide Factsheets

Time domain reflectometers (TDRs) are sensors that measure the volumetric water content of soils and porous media. The sensors consist of stainless steel rods connected to a circuit board in an epoxy housing. An electromagnetic pulse is propagated along the rods. The time, or period, required for the signal to travel down the rods and back varies with the volumetric water content of the surrounding media and temperature. A calibration curve is needed for the specific media. TDRs were developed mostly for agricultural applications; however, the technology has also been applied to forestry and ecological research. This study demonstrates the use of TDRs for quantifying drainage properties in low impact development (LID) stormwater controls, specifically permeable pavement and rain garden systems. TDRs were successfully used to monitor the responses of urban fill, engineered bioretention media, and the aggregate storage layer under permeable pavement to multiple rain events of varying depth, intensity, and duration. The hydrologic performance of permeable pavement and rain garden systems has previously been quantified for underdrain systems, but there have been few studies of systems that drain to the underlying soils. We know of no published studies outlining the use of TDR technology to document drainage properties in media other than soil. In this study TDRs were installed at multiple locations and depths in underlying urban fill soils, engineered bior

First results of the SOL reflectometer on Alcator C-Mod.

PubMed

Lau, C; Hanson, G; Lin, Y; Wilgen, J; Wukitch, S; Labombard, B; Wallace, G

2012-10-01

A swept-frequency X-mode reflectometer has been built on Alcator C-Mod to measure the scrape-off layer (SOL) density profiles adjacent to the lower hybrid launcher. The reflectometer system operates between 100 and 146 GHz at sweep rates from 10 μs to 1 ms and covers a density range of ∼10(16)-10(20) m(-3) at B(0) = 5-5.4 T. This paper discusses the analysis of reflectometer density profiles and presents first experimental results of SOL density profile modifications due to the application of lower hybrid range-of-frequencies power to L-mode discharges. Comparison between density profiles measured by the X-mode reflectometer and scanning Langmuir probes is also shown.

Portable six-port reflectometer for determining moisture content of biomass material

USDA-ARS?s Scientific Manuscript database

A portable six-port reflectometer (SPR) for determining moisture content of biomass material is proposed for the first time in this paper. The proposed system consists of a 5.13 GHz reflectometer used with an open-ended half-mode substrateintegrated waveguide (HMSIW) sensor. The complex permittivity...

Advanced density profile reflectometry; the state-of-the-art and measurement prospects for ITER

NASA Astrophysics Data System (ADS)

Doyle, E. J.

2006-10-01

Dramatic progress in millimeter-wave technology has allowed the realization of a key goal for ITER diagnostics, the routine measurement of the plasma density profile from millimeter-wave radar (reflectometry) measurements. In reflectometry, the measured round-trip group delay of a probe beam reflected from a plasma cutoff is used to infer the density distribution in the plasma. Reflectometer systems implemented by UCLA on a number of devices employ frequency-modulated continuous-wave (FM-CW), ultrawide-bandwidth, high-resolution radar systems. One such system on DIII-D has routinely demonstrated measurements of the density profile over a range of electron density of 0-6.4x10^19,m-3, with ˜25 μs time and ˜4 mm radial resolution, meeting key ITER requirements. This progress in performance was made possible by multiple advances in the areas of millimeter-wave technology, novel measurement techniques, and improved understanding, including: (i) fast sweep, solid-state, wide bandwidth sources and power amplifiers, (ii) dual polarization measurements to expand the density range, (iii) adaptive radar-based data analysis with parallel processing on a Unix cluster, (iv) high memory depth data acquisition, and (v) advances in full wave code modeling. The benefits of advanced system performance will be illustrated using measurements from a wide range of phenomena, including ELM and fast-ion driven mode dynamics, L-H transition studies and plasma-wall interaction. The measurement capabilities demonstrated by these systems provide a design basis for the development of the main ITER profile reflectometer system. This talk will explore the extent to which these reflectometer system designs, results and experience can be translated to ITER, and will identify what new studies and experimental tests are essential.

Characterization of the Multi-Blade 10B-based detector at the CRISP reflectometer at ISIS for neutron reflectometry at ESS

NASA Astrophysics Data System (ADS)

Piscitelli, F.; Mauri, G.; Messi, F.; Anastasopoulos, M.; Arnold, T.; Glavic, A.; Höglund, C.; Ilves, T.; Lopez Higuera, I.; Pazmandi, P.; Raspino, D.; Robinson, L.; Schmidt, S.; Svensson, P.; Varga, D.; Hall-Wilton, R.

2018-05-01

The Multi-Blade is a Boron-10-based gaseous thermal neutron detector developed to face the challenge arising in neutron reflectometry at neutron sources. Neutron reflectometers are challenging instruments in terms of instantaneous counting rate and spatial resolution. This detector has been designed according to the requirements given by the reflectometers at the European Spallation Source (ESS) in Sweden. The Multi-Blade has been installed and tested on the CRISP reflectometer at the ISIS neutron and muon source in U.K.. The results on the detailed detector characterization are discussed in this manuscript.

Distributed fiber optical sensing of oxygen with optical time domain reflectometry.

PubMed

Eich, Susanne; Schmälzlin, Elmar; Löhmannsröben, Hans-Gerd

2013-05-31

In many biological and environmental applications spatially resolved sensing of molecular oxygen is desirable. A powerful tool for distributed measurements is optical time domain reflectometry (OTDR) which is often used in the field of telecommunications. We combine this technique with a novel optical oxygen sensor dye, triangular-[4] phenylene (TP), immobilized in a polymer matrix. The TP luminescence decay time is 86 ns. The short decay time of the sensor dye is suitable to achieve a spatial resolution of some meters. In this paper we present the development and characterization of a reflectometer in the UV range of the electromagnetic spectrum as well as optical oxygen sensing with different fiber arrangements.

Distributed Fiber Optical Sensing of Oxygen with Optical Time Domain Reflectometry

PubMed Central

Eich, Susanne; Schmälzlin, Elmar; Löhmannsröben, Hans-Gerd

2013-01-01

In many biological and environmental applications spatially resolved sensing of molecular oxygen is desirable. A powerful tool for distributed measurements is optical time domain reflectometry (OTDR) which is often used in the field of telecommunications. We combine this technique with a novel optical oxygen sensor dye, triangular-[4] phenylene (TP), immobilized in a polymer matrix. The TP luminescence decay time is 86 ns. The short decay time of the sensor dye is suitable to achieve a spatial resolution of some meters. In this paper we present the development and characterization of a reflectometer in the UV range of the electromagnetic spectrum as well as optical oxygen sensing with different fiber arrangements. PMID:23727953

Scrape-off layer reflectometer for Alcator C-Mod.

PubMed

Hanson, G R; Wilgen, J B; Lau, C; Lin, Y; Wallace, G M; Wukitch, S J

2008-10-01

A two-frequency x-mode reflectometer operating from 100 to 146 GHz is deployed on Alcator C-Mod to measure the density profile and fluctuations in the scrape-off layer (SOL) immediately in front of the new J-port ICRF antenna and the new C-port lower hybrid launcher. The reflectometer covers densities from 10(16) to 10(20) m(-3) at 5-5.4 T. To provide the greatest flexibility and capability to deal with density fluctuations approaching 100% peak-to-peak in the SOL, both full-phase and differential-phase measurement capabilities with sweep speeds of approximately 10 micros to >1 ms are implemented. The differential-phase measurement uses a difference frequency of 500 MHz, corresponding to cutoff layer separations ranging from about 0.1 to 1 mm. The reflectometer has six sets of launchers: three on the ICRF antenna and three on the lower hybrid launcher. Both the ICRF antenna and the lower hybrid launcher incorporate reflectometer antennas at their top, bottom, and midplane locations.

Experiment Automation with a Robot Arm using the Liquids Reflectometer Instrument at the Spallation Neutron Source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zolnierczuk, Piotr A; Vacaliuc, Bogdan; Sundaram, Madhan

The Liquids Reflectometer instrument installed at the Spallation Neutron Source (SNS) enables observations of chemical kinetics, solid-state reactions and phase-transitions of thin film materials at both solid and liquid surfaces. Effective measurement of these behaviors requires each sample to be calibrated dynamically using the neutron beam and the data acquisition system in a feedback loop. Since the SNS is an intense neutron source, the time needed to perform the measurement can be the same as the alignment process, leading to a labor-intensive operation that is exhausting to users. An update to the instrument control system, completed in March 2013, implementedmore » the key features of automated sample alignment and robot-driven sample management, allowing for unattended operation over extended periods, lasting as long as 20 hours. We present a case study of the effort, detailing the mechanical, electrical and software modifications that were made as well as the lessons learned during the integration, verification and testing process.« less

Simultaneous measurements of X-ray reflectivity and grazing incidence fluorescence at BL-16 beamline of Indus-2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Gangadhar; Kane, S. R.; Khooha, Ajay

2015-05-15

A new multipurpose x-ray reflectometer station has been developed and augmented at the microfocus beamline (BL-16) of Indus-2 synchrotron radiation source to facilitate synchronous measurements of specular x-ray reflectivity and grazing incidence x-ray fluorescence emission from thin layered structures. The design and various salient features of the x-ray reflectometer are discussed. The performance of the reflectometer has been evaluated by analyzing several thin layered structures having different surface interface properties. The results reveal in-depth information for precise determination of surface and interface properties of thin layered materials demonstrating the immense potential of the combined measurements of x-ray reflectivity and grazingmore » incidence fluorescence on a single reflectometer.« less

Longitudinal measurement of chromatic dispersion along an optical fiber transmission system with a new correction factor

NASA Astrophysics Data System (ADS)

Abbasi, Madiha; Imran Baig, Mirza; Shafique Shaikh, Muhammad

2013-12-01

At present existence OTDR based techniques have become a standard practice for measuring chromatic dispersion distribution along an optical fiber transmission link. A constructive measurement technique has been offered in this paper, in which a four wavelength bidirectional optical time domain reflectometer (OTDR) has been used to compute the chromatic dispersion allocation beside an optical fiber transmission system. To improve the correction factor a novel formulation has been developed, which leads to an enhanced and defined measurement. The investigational outcomes obtained are in good harmony.

Analysis of a novel sensor interrogation technique based on fiber cavity ring-down (CRD) loop and OTDR

NASA Astrophysics Data System (ADS)

Yüksel, Kivilcim; Yilmaz, Anil

2018-07-01

We present the analysis of a remote sensor based on fiber Cavity Ring-Down (CRD) loop interrogated by an Optical Time Domain Reflectometer (OTDR) taking into account both practical limitations and the related signal processing. A commercial OTDR is used for both pulse generation and sensor output detection. This allows obtaining a compact and simple design for intensity-based sensor applications. This novel sensor interrogation approach is experimentally demonstrated by placing a variable attenuator inside the fiber loop that mimics a sensor head.

Fiber optic security seal including plural Bragg gratings

DOEpatents

Forman, Peter R.

1994-01-01

An optical security system enables the integrity of a container seal to be remotely interrogated. A plurality of Bragg gratings is written holographically into the core of at least one optical fiber placed about the container seal, where each Bragg grating has a predetermined location and a known frequency for reflecting incident light. A time domain reflectometer is provided with a variable frequency light output that corresponds to the reflecting frequencies of the Bragg gratings to output a signal that is functionally related to the location and reflecting frequency of each of the Bragg gratings.

Applications Of Measurement Techniques To Develop Small-Diameter, Undersea Fiber Optic Cables

NASA Astrophysics Data System (ADS)

Kamikawa, Neil T.; Nakagawa, Arthur T.

1984-12-01

Attenuation, strain, and optical time domain reflectometer (OTDR) measurement techniques were applied successfully in the development of a minimum-diameter, electro-optic sea floor cable. Temperature and pressure models for excess attenuation in polymer coated, graded-index fibers were investigated analytically and experimentally using these techniques in the laboratory. The results were used to select a suitable fiber for the cable. Measurements also were performed on these cables during predeployment and sea-trial testing to verify laboratory results. Application of the measurement techniques and results are summarized in this paper.

ALICE—An advanced reflectometer for static and dynamic experiments in magnetism at synchrotron radiation facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abrudan, R.; Helmholtz-Zentrum-Berlin for Materials and Energy, 12489 Berlin; Brüssing, F.

2015-06-15

We report on significant developments of a high vacuum reflectometer (diffractometer) and spectrometer for soft x-ray synchrotron experiments which allows conducting a wide range of static and dynamic experiments. Although the chamber named ALICE was designed for the analysis of magnetic hetero- and nanostructures via resonant magnetic x-ray scattering, the instrument is not limited to this technique. The versatility of the instrument was testified by a series of pilot experiments. Static measurements involve the possibility to use scattering and spectroscopy synchrotron based techniques (photon-in photon-out, photon-in electron-out, and coherent scattering). Dynamic experiments require either laser or magnetic field pulses tomore » excite the spin system followed by x-ray probe in the time domain from nano- to femtosecond delay times. In this temporal range, the demagnetization/remagnetization dynamics and magnetization precession in a number of magnetic materials (metals, alloys, and magnetic multilayers) can be probed in an element specific manner. We demonstrate here the capabilities of the system to host a variety of experiments, featuring ALICE as one of the most versatile and demanded instruments at the Helmholtz Center in Berlin-BESSY II synchrotron center in Berlin, Germany.« less

Methods to Determine the Deformation of the IRVE Hypersonic Inflatable Aerodynamic Decelerator

NASA Technical Reports Server (NTRS)

Young, William R.

2011-01-01

Small resonant targets used in conjunction with a microwave reflectometer to determine the deformation of the Hypersonic Inflatable Aerodynamic Decelerator (HIAD) during reentry are investigated. The reflectometer measures the distance to the targets and from this the HIAD deformation is determined. The HIAD is used by the Inflatable Reentry Vehicle Experiment (IRVE) which investigates the use of inflatable heat shields for atmospheric reentry. After several different microwave reflectometer systems were analyzed and compared it was determined that the most desirable for this application is the Frequency Doubling Target method.

NIST High Accuracy Reference Reflectometer-Spectrophotometer

PubMed Central

Proctor, James E.; Yvonne Barnes, P.

1996-01-01

A new reflectometer-spectrophotometer has been designed and constructed using state-of-the-art technology to enhance optical properties of materials measurements over the ultraviolet, visible, and near-infrared (UV-Vis-NIR) wavelength range (200 nm to 2500 nm). The instrument, Spectral Tri-function Automated Reference Reflectometer (STARR), is capable of measuring specular and diffuse reflectance, bidirectional reflectance distribution function (BRDF) of diffuse samples, and both diffuse and non-diffuse transmittance. Samples up to 30 cm by 30 cm can be measured. The instrument and its characterization are described. PMID:27805081

Monitoring technique for a hybrid PS/WDM-PON by using a tunable OTDR and FBGs

NASA Astrophysics Data System (ADS)

Hann, Swook; Yoo, Jun-sang; Park, Chang-Soo

2006-05-01

A monitoring technique for hybrid passive optical networks (PON) is presented. The technique is based on the remote sensing of fibre Bragg gratings (FBGs) using a tunable optical time domain reflectometer (OTDR). The FBG would help discern an individual event during the monitoring of the hybrid PON in collaboration with the information provided by the Rayleigh backscattered power. The hybrid architecture of passive splitter-PON and WDM-PON can be analysed by the monitoring method by using the tunable OTDR and FBGs at the central office under the in-service state of PON.

Fiber optic security seal including plural Bragg gratings

DOEpatents

Forman, P.R.

1994-09-27

An optical security system enables the integrity of a container seal to be remotely interrogated. A plurality of Bragg gratings is written holographically into the core of at least one optical fiber placed about the container seal, where each Bragg grating has a predetermined location and a known frequency for reflecting incident light. A time domain reflectometer is provided with a variable frequency light output that corresponds to the reflecting frequencies of the Bragg gratings to output a signal that is functionally related to the location and reflecting frequency of each of the Bragg gratings. 2 figs.

Optimal design of reflectometer density profile measurements using a radar systems approach (invited) (abstract)

NASA Astrophysics Data System (ADS)

Doyle, E. J.; Kim, K. W.; Peebles, W. A.; Rhodes, T. L.

1997-01-01

Reflectometry is an attractive and versatile diagnostic technique that can address a wide range of measurement needs on fusion devices. However, progress in the area of profile measurement has been hampered by the lack of a well-understood basis for the optimum design and implementation of such systems. Such a design basis is provided by the realization that reflectometer systems utilized for density profile measurements are in fact specialized forms of radar systems. In this article five criteria are introduced by which reflectometer systems can be systematically designed for optimal performance: range resolution, spatial sampling, turbulence immunity, bandwidth optimization, and the need for adaptive data processing. Many of these criteria are familiar from radar systems analysis, and are applicable to reflectometry after allowance is made for differences stemming from the nature of the plasma target. These criteria are utilized to critically evaluate current reflectometer density profile techniques and indicate improvements that can impact current and next step devices, such as ITER.

Development of frequency modulation reflectometer for KSTAR tokamak: Data analysis based on Gaussian derivative waveleta)

NASA Astrophysics Data System (ADS)

Seo, Seong-Heon; Lee, K. D.

2012-10-01

A frequency modulation reflectometer has been developed to measure the density profile of the KSTAR tokamak. It has two channels operating in X-mode in the frequency range of Q band (33-50 GHz) and V band (50-75 GHz). The full band is swept in 20 μs. The mixer output is directly digitized at the sampling rate of 100 MSamples/s. A new phase detection algorithm is developed to analyze both amplitude and frequency modulated signal. The algorithm is benchmarked for a synthesized amplitude modulation-frequency modulation signal. This new algorithm is applied to the data analysis of KSTAR reflectometer.

Development of Surfaces Optically Suitable for Flat Solar Panels. [using a reflectometer which separately evaluates spectral and diffuse reflectivities of surfaces

NASA Technical Reports Server (NTRS)

1979-01-01

A reflectometer which can separately evaluate the spectral and diffuse reflectivities of surfaces is described. A phase locked detection system for the reflectometer is also described. A selective coating on aluminum potentially useful for flat plate solar collector applications is presented. The coating is composed of strongly bound copper oxide (divalent) and is formed by an etching process performed on an aluminum alloy with high copper content. Fabrication costs are expected to be small due to the one stop fabrication process. A number of conclusions gathered from the literature as to the required optical properties of flat plate solar collectors are discussed.

A novel technique for real-time estimation of edge pedestal density gradients via reflectometer time delay data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeng, L., E-mail: zeng@fusion.gat.com; Doyle, E. J.; Rhodes, T. L.

2016-11-15

A new model-based technique for fast estimation of the pedestal electron density gradient has been developed. The technique uses ordinary mode polarization profile reflectometer time delay data and does not require direct profile inversion. Because of its simple data processing, the technique can be readily implemented via a Field-Programmable Gate Array, so as to provide a real-time density gradient estimate, suitable for use in plasma control systems such as envisioned for ITER, and possibly for DIII-D and Experimental Advanced Superconducting Tokamak. The method is based on a simple edge plasma model with a linear pedestal density gradient and low scrape-off-layermore » density. By measuring reflectometer time delays for three adjacent frequencies, the pedestal density gradient can be estimated analytically via the new approach. Using existing DIII-D profile reflectometer data, the estimated density gradients obtained from the new technique are found to be in good agreement with the actual density gradients for a number of dynamic DIII-D plasma conditions.« less

Temperature measurements in an ytterbium fiber amplifier up to the mode instability threshold

NASA Astrophysics Data System (ADS)

Beier, F.; Heinzig, M.; Sattler, Bettina; Walbaum, Till; Haarlammert, N.; Schreiber, T.; Eberhardt, R.; Tünnermann, A.

2016-03-01

We report on the measurement of the longitudinal temperature distribution in a fiber amplifier fiber during high power operation. The measurement signal of an optical frequency domain reflectometer is coupled to an ytterbium doped amplifier fiber via a wavelength division multiplexer. The longitudinal temperature distribution was examined for different pump powers with a sub mm resolution. The results show even small temperature variations induced by slight changes of the environmental conditions along the fiber. The mode instability threshold of the fiber under investigation was determined to be 480W and temperatures could be measured overall the measured output power values.

Technique for finding and identifying filters that cut off OTDR lights in front of ONU from a central office

NASA Astrophysics Data System (ADS)

Takaya, Masaaki; Honda, Hiroyasu; Narita, Yoshihiro; Yamamoto, Fumihiko; Arakawa, Koji

2006-04-01

We report on a newly developed in-service measurement technique that can be used from a central office to find and identify any filter in front of an ONU on an optical fiber access network. Using this system, in-service tests can be performed because the test lights are modulated at a high frequency. Moreover, by using the equipment we developed, this confirmation operation can be performed continuously and automatically with existing automatic fiber testing systems. The developed technique is effective for constructing a fiber line testing system with an optical time domain reflectometer.

Method and apparatus for active tamper indicating device using optical time-domain reflectometry

DOEpatents

Smith, D. Barton; Muhs, Jeffrey D.; Pickett, Chris A.; Earl, D. Duncan

1999-01-01

An optical time-domain reflectometer (OTDR) launches pulses of light into a link or a system of multiplexed links and records the waveform of pulses reflected by the seals in the link(s). If a seal is opened, the link of cables will become a discontinuous transmitter of the light pulses and the OTDR can immediately detect that a seal has been opened. By analyzing the waveform, the OTDR can also quickly determine which seal(s) were opened. In this way the invention functions as a system of active seals. The invention is intended for applications that require long-term surveillance of a large number of closures. It provides immediate tamper detection, allows for periodic access to secured closures, and can be configured for many different distributions of closures. It can monitor closures in indoor and outdoor locations and it can monitor containers or groups of containers located many kilometers apart.

2D microwave imaging reflectometer electronics.

PubMed

Spear, A G; Domier, C W; Hu, X; Muscatello, C M; Ren, X; Tobias, B J; Luhmann, N C

2014-11-01

A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

Metal-coated Bragg grating reflecting fibre

NASA Astrophysics Data System (ADS)

Chamorovskiy, Yu. K.; Butov, O. V.; Kolosovskiy, A. O.; Popov, S. M.; Voloshin, V. V.; Vorob'ev, I. L.; Vyatkin, M. Yu.

2017-03-01

High-temperature optical fibres (OF) with fibre Bragg gratings (FBG) arrays written over a long length and in-line metal coating have been made for the first time. The optical parameters of the FBG arrays were tested by the optical frequency domain reflectometer (OFDR) method in a wide temperature range, demonstrating no degradation in reflection at heating up to 600 °C for a fibre with Al coating. The mechanical strength of the developed fibre was practically the same as "ordinary" OF with similar coating, showing the absence of the influence of FBG writing process on fibre strength. Further experiments are necessary to evaluate the possibility of further increases in the operational temperature range.

Novel analysis technique for measuring edge density fluctuation profiles with reflectometry in the Large Helical Device.

PubMed

Creely, A J; Ida, K; Yoshinuma, M; Tokuzawa, T; Tsujimura, T; Akiyama, T; Sakamoto, R; Emoto, M; Tanaka, K; Michael, C A

2017-07-01

A new method for measuring density fluctuation profiles near the edge of plasmas in the Large Helical Device (LHD) has been developed utilizing reflectometry combined with pellet-induced fast density scans. Reflectometer cutoff location was calculated by proportionally scaling the cutoff location calculated with fast far infrared laser interferometer (FIR) density profiles to match the slower time resolution results of the ray-tracing code LHD-GAUSS. Plasma velocity profile peaks generated with this reflectometer mapping were checked against velocity measurements made with charge exchange spectroscopy (CXS) and were found to agree within experimental uncertainty once diagnostic differences were accounted for. Measured density fluctuation profiles were found to peak strongly near the edge of the plasma, as is the case in most tokamaks. These measurements can be used in the future to inform inversion methods of phase contrast imaging (PCI) measurements. This result was confirmed with both a fixed frequency reflectometer and calibrated data from a multi-frequency comb reflectometer, and this method was applied successfully to a series of discharges. The full width at half maximum of the turbulence layer near the edge of the plasma was found to be only 1.5-3 cm on a series of LHD discharges, less than 5% of the normalized minor radius.

Measurement of ICRF wave propagation using a microwave reflectometer with fast antenna switching on GAMMA 10

NASA Astrophysics Data System (ADS)

Ikezoe, R.; Ichimura, M.; Itagaki, J.; Hirata, M.; Sumida, S.; Jang, S.; Izumi, K.; Tanaka, A.; Sekine, R.; Kubota, Y.; Shima, Y.; Kohagura, J.; Yoshikawa, M.; Sakamoto, M.; Nakashima, Y.

2017-12-01

Slow Alfvén wave in ion cyclotron range of frequency (ICRF) is a powerful tool to heat ions confined in a mirror field. In spite of its efficient heating effect that has been attained in the central cell of GAMMA 10, there are still unknown characteristics concerning boundary condition, transient variation of heating effect, exact picture of cyclotron damping, and so on. To study these characteristics in detail, a multi-point measurement of the waves inside the hot plasma has been recently developed by using a microwave reflectometer. In addition to a radial profile measurement that is available by a usual reflectometer, an axial measurement has been achieved by arraying transmitting and receiving horn antennas in the axial direction, which are repeatedly switched in time during a discharge with PIN diode switches. Another transmitting and receiving horn antenna pair was newly added to the system and probing at five cross sections was achieved in a single discharge with time resolution of about 1 ms at each antenna pair position. With the upgraded reflectometer system, axial and radial distributions of wave-induced fluctuations and those temporal behavior were clearly observed, offering valuable data on wave physics in a hot mirror plasma.

Novel analysis technique for measuring edge density fluctuation profiles with reflectometry in the Large Helical Device

NASA Astrophysics Data System (ADS)

Creely, A. J.; Ida, K.; Yoshinuma, M.; Tokuzawa, T.; Tsujimura, T.; Akiyama, T.; Sakamoto, R.; Emoto, M.; Tanaka, K.; Michael, C. A.

2017-07-01

A new method for measuring density fluctuation profiles near the edge of plasmas in the Large Helical Device (LHD) has been developed utilizing reflectometry combined with pellet-induced fast density scans. Reflectometer cutoff location was calculated by proportionally scaling the cutoff location calculated with fast far infrared laser interferometer (FIR) density profiles to match the slower time resolution results of the ray-tracing code LHD-GAUSS. Plasma velocity profile peaks generated with this reflectometer mapping were checked against velocity measurements made with charge exchange spectroscopy (CXS) and were found to agree within experimental uncertainty once diagnostic differences were accounted for. Measured density fluctuation profiles were found to peak strongly near the edge of the plasma, as is the case in most tokamaks. These measurements can be used in the future to inform inversion methods of phase contrast imaging (PCI) measurements. This result was confirmed with both a fixed frequency reflectometer and calibrated data from a multi-frequency comb reflectometer, and this method was applied successfully to a series of discharges. The full width at half maximum of the turbulence layer near the edge of the plasma was found to be only 1.5-3 cm on a series of LHD discharges, less than 5% of the normalized minor radius.

Proof of Concept: Development of Snow Liquid Water Content Profiler Using CS650 Reflectometers at Caribou, ME, USA.

PubMed

Pérez Díaz, Carlos L; Muñoz, Jonathan; Lakhankar, Tarendra; Khanbilvardi, Reza; Romanov, Peter

2017-03-21

The quantity of liquid water in the snowpack defines its wetness. The temporal evolution of snow wetness's plays a significant role in wet-snow avalanche prediction, meltwater release, and water availability estimations and assessments within a river basin. However, it remains a difficult task and a demanding issue to measure the snowpack's liquid water content (LWC) and its temporal evolution with conventional in situ techniques. We propose an approach based on the use of time-domain reflectometry (TDR) and CS650 soil water content reflectometers to measure the snowpack's LWC and temperature profiles. For this purpose, we created an easily-applicable, low-cost, automated, and continuous LWC profiling instrument using reflectometers at the Cooperative Remote Sensing Science and Technology Center-Snow Analysis and Field Experiment (CREST-SAFE) in Caribou, ME, USA, and tested it during the snow melt period (February-April) immediately after installation in 2014. Snow Thermal Model (SNTHERM) LWC simulations forced with CREST-SAFE meteorological data were used to evaluate the accuracy of the instrument. Results showed overall good agreement, but clearly indicated inaccuracy under wet snow conditions. For this reason, we present two (for dry and wet snow) statistical relationships between snow LWC and dielectric permittivity similar to Topp's equation for the LWC of mineral soils. These equations were validated using CREST-SAFE in situ data from winter 2015. Results displayed high agreement when compared to LWC estimates obtained using empirical formulas developed in previous studies, and minor improvement over wet snow LWC estimates. Additionally, the equations seemed to be able to capture the snowpack state (i.e., onset of melt, medium, and maximum saturation). Lastly, field test results show advantages, such as: automated, continuous measurements, the temperature profiling of the snowpack, and the possible categorization of its state. However, future work should focus on improving the instrument's capability to measure the snowpack's LWC profile by properly calibrating it with in situ LWC measurements. Acceptable validation agreement indicates that the developed snow LWC, temperature, and wetness profiler offers a promising new tool for snow hydrology research.

At-wavelength metrology facility for soft X-ray reflection optics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sokolov, A., E-mail: andrey.sokolov@helmholtz-berlin.de; Bischoff, P.; Eggenstein, F.

2016-05-15

A new Optics Beamline coupled to a versatile UHV reflectometer is successfully operating at BESSY-II. It is used to carry out at-wavelength characterization and calibration of in-house produced gratings and novel nano-optical devices as well as mirrors and multilayer systems in the UV and XUV spectral region. This paper presents most recent commissioning data of the beamline and shows their correlation with initial beamline design calculations. Special attention is paid to beamline key parameters which determine the quality of the measurements such as high-order suppression and stray light behavior. The facility is open to user operation.

Coal-shale interface detection system

NASA Technical Reports Server (NTRS)

Campbell, R. A.; Hudgins, J. L.; Morris, P. W.; Reid, H., Jr.; Zimmerman, J. E. (Inventor)

1979-01-01

A coal-shale interface detection system for use with coal cutting equipment consists of a reciprocating hammer on which an accelerometer is mounted to measure the impact of the hammer as it penetrates the ceiling or floor surface of a mine. A pair of reflectometers simultaneously view the same surface. The outputs of the accelerometer and reflectometers are detected and jointly registered to determine when an interface between coal and shale is being cut through.

Coal-shale interface detector

NASA Technical Reports Server (NTRS)

Reid, H., Jr. (Inventor)

1980-01-01

A coal-shale interface detector for use with coal cutting equipment is described. The detector consists of a reciprocating hammer with an accelerometer to measure the impact of the hammer as it penetrates the ceiling or floor surface of a mine. Additionally, a pair of reflectometers simultaneously view the same surface, and the outputs from the accelerometer and reflectometers are detected and jointly registered to determine when an interface between coal and shale is being cut through.

Optimization studies of the ITER low field side reflectometer.

PubMed

Diem, S J; Wilgen, J B; Bigelow, T S; Hanson, G R; Harvey, R W; Smirnov, A P

2010-10-01

Microwave reflectometry will be used on ITER to measure the electron density profile, density fluctuations due to MHD/turbulence, edge localized mode (ELM) density transients, and as an L-H transition monitor. The ITER low field side reflectometer system will measure both core and edge quantities using multiple antenna arrays spanning frequency ranges of 15-155 GHz for the O-mode system and 55-220 GHz for the X-mode system. Optimization studies using the GENRAY ray-tracing code have been done for edge and core measurements. The reflectometer launchers will utilize the HE11 mode launched from circular corrugated waveguide. The launched beams are assumed to be Gaussian with a beam waist diameter of 0.643 times the waveguide diameter. Optimum launcher size and placement are investigated by computing the antenna coupling between launchers, assuming the launched and received beams have a Gaussian beam pattern.

Study of coherent reflectometer for imaging internal structures of highly scattering media

NASA Astrophysics Data System (ADS)

Poupardin, Mathieu; Dolfi, Agnes

1996-01-01

Optical reflectometers are potentially useful tools for imaging internal structures of turbid media, particularly of biological media. To get a point by point image, an active imaging system has to distinguish light scattered from a sample volume and light scattered by other locations in the media. Operating this discrimination of light with reflectometers based on coherence can be realized in two ways: assuring a geometric selection or a temporal selection. In this paper we present both methods, showing in each case the influence of the different parameters on the size of the sample volume under the assumption of single scattering. We also study the influence on the detection efficiency of the coherence loss of the incident light resulting from multiple scattering. We adapt a model, first developed for atmospheric lidar in turbulent atmosphere, to get an analytical expression of this detection efficiency in the function of the optical coefficients of the media.

Catheter guided by optical coherence domain reflectometry

DOEpatents

Everett, Matthew; Colston, Billy W.; Da Silva, Luiz B.; Matthews, Dennis

2002-01-01

A guidance and viewing system based on multiplexed optical coherence domain reflectometry is incorporated into a catheter, endoscope, or other medical device to measure the location, thickness, and structure of the arterial walls or other intra-cavity regions at discrete points on the medical device during minimally invasive medical procedures. The information will be used both to guide the device through the body and to evaluate the tissue through which the device is being passed. Multiple optical fibers are situated along the circumference of the device. Light from the distal end of each fiber is directed onto the interior cavity walls via small diameter optics (such as gradient index lenses and mirrored corner cubes). Both forward viewing and side viewing fibers can be included. The light reflected or scattered from the cavity walls is then collected by the fibers and multiplexed at the proximal end to the sample arm of an optical low coherence reflectometer. The system may also be implemented in a nonmedical inspection device.

AWG-based WDM-PON monitoring system using an optical switch and a WDM filter

NASA Astrophysics Data System (ADS)

Liaw, S.-K.; Lai, Y.-T.; Chang, C.-L.; Shung, O.

2008-09-01

A new WDM-PON scheme with real-time monitoring based on a time-sharing method is proposed. It uses an optical time domain reflectometer (OTDR) to monitor multiple ports by integrating an optical switch (OSW) with a dense wavelength division multiplexer (DWDM) at the optical line terminal (OLT) site. Each downstream signal and its corresponding monitoring signal are separated by m times the free-space range (FSR) of an array waveguide grating (AWG). A bit error rate (BER) test in 2.5 Gb/s × 27 km is performed with and without turning on the OTDR. A small power penalty of 0.7 dB is observed compared to the back-to-back measurement.

Automated data acquisition and processing for a Hohlraum reflectometer

NASA Technical Reports Server (NTRS)

Difilippo, Frank; Mirtich, Michael J.

1988-01-01

A computer and data acquisition board were used to automate a Perkin-Elmer Model 13 spectrophotometer with a Hohlraum reflectivity attachment. Additional electronic circuitry was necessary for amplification, filtering, and debouncing. The computer was programmed to calculate spectral emittance from 1.7 to 14.7 micrometers and also total emittance versus temperature. Automation of the Hohlraum reflectometer reduced the time required to determine total emittance versus temperature from about three hours to about 40 minutes.

Coal-shale interface detection

NASA Technical Reports Server (NTRS)

Broussard, P. H.; Burch, J. L.; Drost, E. J.; Stein, R. J. (Inventor)

1979-01-01

A penetrometer for coal-shale interface detection is presented. It is used with coal cutting equipment consisting of a reciprocating hammer, having an accelerometer mounted thereon to measure the impact of the hammer as it penetrates the ceiling or floor surface of a mine. Additionally, a pair of reflectometers simultaneously view the same surface, and the outputs from the accelerometer and reflectometers are detected and jointly registered to determine when an interface between coal and shale is being cut through.

Tear film measurement by optical reflectometry technique

PubMed Central

Lu, Hui; Wang, Michael R.; Wang, Jianhua; Shen, Meixiao

2014-01-01

Abstract. Evaluation of tear film is performed by an optical reflectometer system with alignment guided by a galvanometer scanner. The reflectometer system utilizes optical fibers to deliver illumination light to the tear film and collect the film reflectance as a function of wavelength. Film thickness is determined by best fitting the reflectance-wavelength curve. The spectral reflectance acquisition time is 15 ms, fast enough for detecting film thickness changes. Fast beam alignment of 1 s is achieved by the galvanometer scanner. The reflectometer was first used to evaluate artificial tear film on a model eye with and without a contact lens. The film thickness and thinning rate have been successfully quantified with the minimum measured thickness of about 0.3 μm. Tear films in human eyes, with and without a contact lens, have also been evaluated. A high-contrast spectral reflectance signal from the precontact lens tear film is clearly observed, and the thinning dynamics have been easily recorded from 3.69 to 1.31 μm with lipid layer thickness variation in the range of 41 to 67 nm. The accuracy of the measurement is better than ±0.58% of the film thickness at an estimated tear film refractive index error of ±0.001. The fiber-based reflectometer system is compact and easy to handle. PMID:24500519

Analysis of the ITER low field side reflectometer transmission line system.

PubMed

Hanson, G R; Wilgen, J B; Bigelow, T S; Diem, S J; Biewer, T M

2010-10-01

A critical issue in the design of the ITER low field side reflectometer is the transmission line (TL) system. A TL connects each launcher to a diagnostic instrument. Each TL will typically consist of ∼42 m of corrugated waveguide and up to ten miter bends. Important issues for the performance of the TL system are mode conversion and reflections. Minimizing these issues are critical to minimizing standing waves and phase errors. The performance of TL system is analyzed and recommendations are given.

Improved integrating-sphere throughput with a lens and nonimaging concentrator.

PubMed

Chenault, D B; Snail, K A; Hanssen, L M

1995-12-01

A reflectometer design utilizing an integrating sphere with a lens and nonimaging concentrator is described. Compared with previous designs where a collimator was used to restrict the detector field of view, the concentrator-lens combination significantly increases the throughput of the reflectometer. A procedure for designing lens-concentrators is given along with the results of parametric studies. The measured angular response of a lens-concentrator system is compared with ray-trace predictions and with the response of an ideal system.

Microwave reflectometer ionization sensor

NASA Technical Reports Server (NTRS)

Seals, Joseph; Fordham, Jeffrey A.; Pauley, Robert G.; Simonutti, Mario D.

1993-01-01

The development of the Microwave Reflectometer Ionization Sensor (MRIS) Instrument for use on the Aeroassist Flight Experiment (AFE) spacecraft is described. The instrument contract was terminated, due to cancellation of the AFE program, subsequent to testing of an engineering development model. The MRIS, a four-frequency reflectometer, was designed for the detection and location of critical electron density levels in spacecraft reentry plasmas. The instrument would sample the relative magnitude and phase of reflected signals at discrete frequency steps across 4 GHz bandwidths centered at four frequencies: 20, 44, 95, and 140 GHz. The sampled data would be stored for later processing to calculate the distance from the spacecraft surface to the critical electron densities versus time. Four stepped PM CW transmitter receivers were located behind the thermal protection system of the spacecraft with horn antennas radiating and receiving through an insulating tile. Techniques were developed to deal with interference, including multiple reflections and resonance effects, resulting from the antenna configuration and operating environment.

Development of a spatially resolved reflectometer to monitor corrosion of solar reflectors

NASA Astrophysics Data System (ADS)

Sutter, Florian; Meyen, Stephanie; Heller, Peter; Pitz-Paal, Robert

2013-06-01

Solar reflectors for Concentrating Solar Power (CSP) concentrators require a high reflectance and high specularity over the whole solar spectrum. During their lifetime of at least 20 years, the reflectors must withstand harsh outdoor conditions without loosing their reflective properties. Currently, there are not many devices available to measure the specular reflectance. In this work a prototype of a specular reflectometer with spatial resolution has been developed. The major advantage of the prototype compared to other reflectometers is the possibility of measuring the specular reflectance on an extended measuring spot of more than 5 cm in diameter with a spatial resolution of 37 pixel/mm. Additionally, measurements can be taken at three different acceptance half angles (φ = 3.5, 6.0, and 12.5 mrad) and at three different wavelengths (λ = 410 nm, 500 nm, and 656 nm). This lab scale instrument can be employed to monitor degradation effects, such as corrosion spots, and evaluate their influence on the specular reflectance of solar mirror materials.

SuperADAM: Upgraded polarized neutron reflectometer at the Institut Laue-Langevin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devishvili, A.; Zhernenkov, K.; Institut Laue-Langevin, BP 156, 38042 Grenoble

2013-02-15

A new neutron reflectometer SuperADAM has recently been built and commissioned at the Institut Laue-Langevin, Grenoble, France. It replaces the previous neutron reflectometer ADAM. The new instrument uses a solid state polarizer/wavelength filter providing a highly polarized (up to 98.6%) monochromatic neutron flux of 8 Multiplication-Sign 10{sup 4} n cm{sup -2} s{sup -1} with monochromatization {Delta}{lambda}/{lambda}= 0.7% and angular divergence {Delta}{alpha}= 0.2 mrad. The instrument includes both single and position sensitive detectors. The position sensitive detector allows simultaneous measurement of specular reflection and off-specular scattering. Polarization analysis for both specular reflection and off-specular scattering is achieved using either mirror analyzersmore » or a {sup 3}He spin filter cell. High efficiency detectors, low background, and high flux provides a dynamic range of up to seven decades in reflectivity. Detailed specifications and the instrument capabilities are illustrated with examples of recently collected data in the fields of thin film magnetism and thin polymer films.« less

SuperADAM: Upgraded polarized neutron reflectometer at the Institut Laue-Langevin

NASA Astrophysics Data System (ADS)

Devishvili, A.; Zhernenkov, K.; Dennison, A. J. C.; Toperverg, B. P.; Wolff, M.; Hjörvarsson, B.; Zabel, H.

2013-02-01

A new neutron reflectometer SuperADAM has recently been built and commissioned at the Institut Laue-Langevin, Grenoble, France. It replaces the previous neutron reflectometer ADAM. The new instrument uses a solid state polarizer/wavelength filter providing a highly polarized (up to 98.6%) monochromatic neutron flux of 8 × 104 n cm-2 s-1 with monochromatization Δλ/λ = 0.7% and angular divergence Δα = 0.2 mrad. The instrument includes both single and position sensitive detectors. The position sensitive detector allows simultaneous measurement of specular reflection and off-specular scattering. Polarization analysis for both specular reflection and off-specular scattering is achieved using either mirror analyzers or a 3He spin filter cell. High efficiency detectors, low background, and high flux provides a dynamic range of up to seven decades in reflectivity. Detailed specifications and the instrument capabilities are illustrated with examples of recently collected data in the fields of thin film magnetism and thin polymer films.

SuperADAM: upgraded polarized neutron reflectometer at the Institut Laue-Langevin.

PubMed

Devishvili, A; Zhernenkov, K; Dennison, A J C; Toperverg, B P; Wolff, M; Hjörvarsson, B; Zabel, H

2013-02-01

A new neutron reflectometer SuperADAM has recently been built and commissioned at the Institut Laue-Langevin, Grenoble, France. It replaces the previous neutron reflectometer ADAM. The new instrument uses a solid state polarizer/wavelength filter providing a highly polarized (up to 98.6%) monochromatic neutron flux of 8 × 10(4) n cm(-2) s(-1) with monochromatization Δλ∕λ = 0.7% and angular divergence Δα = 0.2 mrad. The instrument includes both single and position sensitive detectors. The position sensitive detector allows simultaneous measurement of specular reflection and off-specular scattering. Polarization analysis for both specular reflection and off-specular scattering is achieved using either mirror analyzers or a (3)He spin filter cell. High efficiency detectors, low background, and high flux provides a dynamic range of up to seven decades in reflectivity. Detailed specifications and the instrument capabilities are illustrated with examples of recently collected data in the fields of thin film magnetism and thin polymer films.

Development of the low-field side reflectometer for ITER

NASA Astrophysics Data System (ADS)

Muscatello, Christopher; Anderson, James; Gattuso, Anthony; Doyle, Edward; Peebles, William; Seraydarian, Raymond; Wang, Guiding; Kramer, Gerrit; Zolfaghari, Ali; Atomics Team, General; University of California Los Angeles Team; Princeton Plasma Physics Laboratory Team

2017-10-01

The Low-Field Side Reflectometer (LFSR) for ITER will provide real-time edge density profiles every 10 ms for feedback control and every 24 μs for physics evaluation. The spatial resolution will be better than 5 mm over 30 - 165 GHz, probing the scrape-off layer to the top of the pedestal in H-mode plasmas. An antenna configuration has been selected for measurements covering anticipated plasma elevations. Laboratory validation of diagnostic performance is underway using a LFSR transmission line (TL) mockup. The 40-meter TL includes circular corrugated waveguide, length calibration feature, Gaussian telescope, vacuum windows, containment membranes, and expansion joint. Transceiver modules coupled to the input of the TL provide frequency-modulated (FM) data for evaluation of performance as a monostatic reflectometer. Results from the mockup tests are presented and show that, with some further optimization, the LFSR will meet or exceed the measurement requirements for ITER. An update of the LFSR instrumentation design status is also presented with preliminary test results. Work supported by PPPL under subcontract S013252-A.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, X.; Yao, C.

A prototype dual-blade stripline kicker for the APS multi-bend achromat (MBA) upgrade has been designed and developed. It was optimized with 3D CST Microwave Studio. The high voltage (HV) feedthrough and air-side connector were designed and optimized. Electromagnetic fields along the beam path, the deflecting angle, the high electric fields and their locations were calculated with 15kV differential pulse voltage applied to the kicker blades through the feedthroughs. Beam impedance and the power dissipation on different parts of the kicker and external loads were studied for a 48-bunch fill pattern. Our results show that the prototype kicker with its HVmore » feedthroughs meets the specified requirements. The results of TDR (time-domain reflectometer) test, high voltage pulse test and beam test of the prototype kicker assembly agreed with the simulations.« less

Calibration Procedure for Measuring S-Parameters in Balun Applications on 150-ohm High-Speed Cables

NASA Technical Reports Server (NTRS)

Theofylaktos, Onoufrios; Warner, Joseph D.

2012-01-01

In the radiofrequency (RF) world, in order to characterize cables that do not conform to the typical 50-omega impedance, a time domain reflectometer (TDR) would probably be the simplest and quickest tool to attain this goal. In the real world, not every engineer has a TDR at their disposal; however, they most likely have a network analyzer available. Given a generic 50-omega vector network analyzer (VNA), we would like to make S-parameter measurements for non-50-omega devices (DUTs). For that, we utilize RF balanced/unbalanced transformers (called baluns for short), which are primarily used to match the impedance between the two VNA ports and the DUT's input and output ports, for the two-port S-parameter measurements.

Development of a distributed polarization-OTDR to measure two vibrations with the same frequency

NASA Astrophysics Data System (ADS)

Pan, Yun; Wang, Feng; Wang, Xiangchuan; Zhang, Mingjiang; Zhou, Ling; Sun, Zhenqing; Zhang, Xuping

2015-08-01

A polarization optical time-domain reflectometer (POTDR) can distributedly measure the vibration of fiber by detecting the vibration induced polarization variation only with a polarization analyzer. It has great potential in the monitoring of the border intrusion, structural healthy, anti-stealing of pipeline and so on, because of its simple configuration, fast response speed and distributed measuring ability. However, it is difficult to distinguish two vibrations with the same frequency for POTDR because the signal induced by the first vibration would bury the other vibration induced signal. This paper proposes a simple method to resolve this problem in POTDR by analyzing the phase of the vibration induced signal. The effectiveness of this method in distinguishing two vibrations with the same frequency for POTDR is proved by simulation.

151-km single-end phase-sensitive optical time-domain reflectometer assisted by optical repeater

NASA Astrophysics Data System (ADS)

Song, Muping; Zhu, Weiji; Xia, Qiaolan; Yin, Cong; Lu, Yan; Wu, Ying; Zhuang, Shouwang

2018-02-01

A phase-sensitive optical time-domain reflectometry (ϕOTDR) system that can detect intrusion over 150 km is presented. The ϕOTDR system uses nonbalanced optical repeaters to extend the sensing distance. The repeater consists of two erbium-doped optical fiber amplifiers (EDFAs) and one Raman amplifier (RA). One EDFA power amplifier amplifies the forward-transmitting pulse, and one EDFA preamplifier is used for the backscattering signal, respectively. The RA helps keeping the power along the fiber stable. The optical repeater is installed at the connection of two adjacent fibers to compensate the power decline due to fiber loss. It is easy to install the repeater midway among the fiber links in the system for longer-distance sensing since there is no need of modifying the original sensing system. The theoretical analysis of the repeater is given to describe its effect on the distributed sensing. In experiments, several ϕOTDR traces show a good agreement with theoretical results. Using the optical repeater, 35-Hz vibration at 151 km is successfully measured with signal-to-noise ratio of 8 dB without extra signal processing.

Robot-assisted motor activation monitored by time-domain optical brain imaging

NASA Astrophysics Data System (ADS)

Steinkellner, O.; Wabnitz, H.; Schmid, S.; Steingräber, R.; Schmidt, H.; Krüger, J.; Macdonald, R.

2011-07-01

Robot-assisted motor rehabilitation proved to be an effective supplement to conventional hand-to-hand therapy in stroke patients. In order to analyze and understand motor learning and performance during rehabilitation it is desirable to develop a monitor to provide objective measures of the corresponding brain activity at the rehabilitation progress. We used a portable time-domain near-infrared reflectometer to monitor the hemodynamic brain response to distal upper extremity activities. Four healthy volunteers performed two different robot-assisted wrist/forearm movements, flexion-extension and pronation-supination in comparison with an unassisted squeeze ball exercise. A special headgear with four optical measurement positions to include parts of the pre- and postcentral gyrus provided a good overlap with the expected activation areas. Data analysis based on variance of time-of-flight distributions of photons through tissue was chosen to provide a suitable representation of intracerebral signals. In all subjects several of the four detection channels showed a response. In some cases indications were found of differences in localization of the activated areas for the various tasks.

Three-Axis Distributed Fiber Optic Strain Measurement in 3D Woven Composite Structures

NASA Technical Reports Server (NTRS)

Castellucci, Matt; Klute, Sandra; Lally, Evan M.; Froggatt, Mark E.; Lowry, David

2013-01-01

Recent advancements in composite materials technologies have broken further from traditional designs and require advanced instrumentation and analysis capabilities. Success or failure is highly dependent on design analysis and manufacturing processes. By monitoring smart structures throughout manufacturing and service life, residual and operational stresses can be assessed and structural integrity maintained. Composite smart structures can be manufactured by integrating fiber optic sensors into existing composite materials processes such as ply layup, filament winding and three-dimensional weaving. In this work optical fiber was integrated into 3D woven composite parts at a commercial woven products manufacturing facility. The fiber was then used to monitor the structures during a VARTM manufacturing process, and subsequent static and dynamic testing. Low cost telecommunications-grade optical fiber acts as the sensor using a high resolution commercial Optical Frequency Domain Reflectometer (OFDR) system providing distributed strain measurement at spatial resolutions as low as 2mm. Strain measurements using the optical fiber sensors are correlated to resistive strain gage measurements during static structural loading. Keywords: fiber optic, distributed strain sensing, Rayleigh scatter, optical frequency domain reflectometry

Feasibility study of the automated detection and localization of underground tunnel excavation using Brillouin optical time domain reflectometer

NASA Astrophysics Data System (ADS)

Klar, Assaf; Linker, Raphael

2009-05-01

Cross-borders smuggling tunnels enable unmonitored movement of people, drugs and weapons and pose a very serious threat to homeland security. Recent advances in strain measurements using optical fibers allow the development of smart underground security fences that could detect the excavation of smuggling tunnels. This paper presents the first stages in the development of such a fence using Brillouin Optical Time Domain Reflectometry (BOTDR). In the simulation study, two different ground displacement models are used in order to evaluate the robustness of the system against imperfect modeling. In both cases, soil-fiber interaction is considered. Measurement errors, and surface disturbances (obtained from a field test) are also included in the calibration and validation stages of the system. The proposed detection system is based on wavelet decomposition of the BOTDR signal, followed by a neural network that is trained to recognize the tunnel signature in the wavelet coefficients. The results indicate that the proposed system is capable of detecting even small tunnel (0.5m diameter) as deep as 20 meter.

Simultaneous measurement of X-ray specular reflection and off-specular diffuse scattering from liquid surfaces using a two-dimensional pixel array detector: the liquid-interface reflectometer of BL37XU at SPring-8.

PubMed

Yano, Yohko F; Uruga, Tomoya; Tanida, Hajime; Toyokawa, Hidenori; Terada, Yasuko; Yamada, Hironari

2010-07-01

An X-ray reflectometer for simultaneous measurement of specular and off-specular reflection of liquid surfaces is described. The reflectometer, equipped with a two-dimensional single X-ray photon-counting pixel array detector obtained the full range of X-ray specular and off-specular reflections in an extremely short time (1 s). Both the specular and off-specular reflection of water exhibited good agreement with the predicted capillary-wave theory within the appropriate instrumental resolution. The approach is also demonstrated on an aqueous solution of 1-dodecyl-3-methylimidazolium chloride. The monolayer in which the dodecyl chain faces upwards and the Cl(-) anion locates next to the imidazolium ring formed on the water surface was found to be laterally homogeneous. The use of a pixel array detector will be particularly powerful for in situ measurements to investigate both out-of-plane and in-plane structures simultaneously, not only for liquid surfaces but also for other thin films.

Design and Validation of a Ten-Port Waveguide Reflectometer Sensor: Application to Efficiency Measurement and Optimization of Microwave-Heating Ovens

PubMed Central

Pedreño-Molina, Juan L.; Monzó-Cabrera, Juan; Lozano-Guerrero, Antonio; Toledo-Moreo, Ana

2008-01-01

This work presents the design, manufacturing process, calibration and validation of a new microwave ten-port waveguide reflectometer based on the use of neural networks. This low-cost novel device solves some of the shortcomings of previous reflectometers such as non-linear behavior of power sensors, noise presence and the complexity of the calibration procedure, which is often based on complex mathematical equations. These problems, which imply the reduction of the reflection coefficient measurement accuracy, have been overcome by using a higher number of probes than usual six-port configurations and by means of the use of Radial Basis Function (RBF) neural networks in order to reduce the influence of noise and non-linear processes over the measurements. Additionally, this sensor can be reconfigured whenever some of the eight coaxial power detectors fail, still providing accurate values in real time. The ten-port performance has been compared against a high-cost measurement instrument such as a vector network analyzer and applied to the measurement and optimization of energy efficiency of microwave ovens, with good results. PMID:27873961

Refractive and relativistic effects on ITER low field side reflectometer design.

PubMed

Wang, G; Rhodes, T L; Peebles, W A; Harvey, R W; Budny, R V

2010-10-01

The ITER low field side reflectometer faces some unique design challenges, among which are included the effect of relativistic electron temperatures and refraction of probing waves. This paper utilizes GENRAY, a 3D ray tracing code, to investigate these effects. Using a simulated ITER operating scenario, characteristics of the reflected millimeter waves after return to the launch plane are quantified as a function of a range of design parameters, including antenna height, antenna diameter, and antenna radial position. Results for edge/SOL measurement with both O- and X-mode polarizations using proposed antennas are reported.

Development of Surfaces Optically Suitable for Flat Solar Panels

NASA Technical Reports Server (NTRS)

Desmet, D.; Jason, A.

1978-01-01

Three areas of research in the development of flat solar panels are described. (1) A reflectometer which can separately evaluate the spectral and diffuse reflectivities of surfaces was developed. The reflectometer has a phase locked detection system. (2) A coating composed of strongly bound copper oxide that is formed by an etching process performed on an aluminum alloy with high copper content was also developed. Because of this one step fabrication process, fabrication costs are expected to be small. (3) A literature search was conducted and conclusions on the required optical properties of flat plate solar collectors are presented.

System and method for determining coolant level and flow velocity in a nuclear reactor

DOEpatents

Brisson, Bruce William; Morris, William Guy; Zheng, Danian; Monk, David James; Fang, Biao; Surman, Cheryl Margaret; Anderson, David Deloyd

2013-09-10

A boiling water reactor includes a reactor pressure vessel having a feedwater inlet for the introduction of recycled steam condensate and/or makeup coolant into the vessel, and a steam outlet for the discharge of produced steam for appropriate work. A fuel core is located within a lower area of the pressure vessel. The fuel core is surrounded by a core shroud spaced inward from the wall of the pressure vessel to provide an annular downcomer forming a coolant flow path between the vessel wall and the core shroud. A probe system that includes a combination of conductivity/resistivity probes and/or one or more time-domain reflectometer (TDR) probes is at least partially located within the downcomer. The probe system measures the coolant level and flow velocity within the downcomer.

Measurement of large strains in ropes using plastic optical fibers

DOEpatents

Williams, Jerry Gene; Smith, David Barton; Muhs, Jeffrey David

2006-02-14

A method for the direct measurement of large strains in ropes in situ using a plastic optical fiber, for example, perfluorocarbon or polymethyl methacrylate and Optical Time-Domain Reflectometer or other light time-of-flight measurement instrumentation. Protective sheaths and guides are incorporated to protect the plastic optical fiber. In one embodiment, a small rope is braided around the plastic optical fiber to impose lateral compressive forces to restrain the plastic optical fiber from slipping and thus experience the same strain as the rope. Methods are described for making reflective interfaces along the length of the plastic optical fiber and to provide the capability to measure strain within discrete segments of the rope. Interpretation of the data allows one to calculate the accumulated strain at any point in time and to determine if the rope has experienced local damage.

Development of frequency modulation reflectometer for Korea Superconducting Tokamak Advanced Research tokamak

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seo, Seong-Heon; Wi, H. M.; Lee, W. R.

2013-08-15

Frequency modulation reflectometer has been developed to measure the plasma density profile of the Korea Superconducting Tokamak Advanced Research tokamak. Three reflectometers are operating in extraordinary polarization mode in the frequency range of Q band (33.6–54 GHz), V band (48–72 GHz), and W band (72–108 GHz) to measure the density up to 7 × 10{sup 19} m{sup −3} when the toroidal magnetic field is 2 T on axis. The antenna is installed inside of the vacuum vessel. A new vacuum window is developed by using 50 μm thick mica film and 0.1 mm thick gold gasket. The filter bank ofmore » low pass filter, notch filter, and Faraday isolator is used to reject the electron cyclotron heating high power at attenuation of 60 dB. The full frequency band is swept in 20 μs. The mixer output is directly digitized with sampling rate of 100 MSamples/s. The phase is obtained by using wavelet transform. The whole hardware and software system is described in detail and the measured density profile is presented as a result.« less

Performance and data analysis aspects of the new DIII-D monostatic profile reflectometer system

DOE PAGES

Zeng, Lei; Peebles, William A.; Doyle, Edward J.; ...

2014-08-07

A new frequency-modulated (FMCW) profile reflectometer system, featuring a monostatic antenna geometry (using one microwave antenna for both launch and receive), has been installed on the DIII-D tokamak, providing a first experimental test of this measurement approach for profile reflectometry. Significant features of the new system are briefly described in this paper, including the new monostatic arrangement, use of overmoded, broadband transmission waveguide, and dual-polarization combination/demultiplexing. Updated data processing and analysis, and in-service performance aspects of the new monostatic profile reflectometer system are also presented. By using a raytracing code (GENRAY) to determine the approximate trajectory of the probe beam,more » the electron density (n e) profile can be successfully reconstructed with L-mode plasmas vertically shifted by more than 10 cm off the vessel midplane. Specifically, it is demonstrated that the new system has a capability to measure n e profiles with plasma vertical offsets of up to ±17 cm. Furthermore, examples are also presented of accurate, high time and spatial resolution density profile measurements made over a wide range of DIII-D conditions, e.g. the measured temporal evolution of the density profile across an L-H transition.« less

The Lunar Prospector Discovery Mission: mission and measurement description.

NASA Astrophysics Data System (ADS)

Hubbard, G. S.; Binder, A. B.; Feldman, W.

1998-06-01

Lunar Prospector, the first competitively selected planetary mission in NASA's Discovery Program, is described with emphasis on the radiation spectrometer instrumentation and anticipated scientific data return. Scheduled to be launched in January 1998, the mission will conduct a one year orbital survey of the Moon's composition and structure. The suite of five instruments are outlined: neutron spectrometer, alpha particle spectrometer, gamma-ray spectrometer, electron reflectometer and magnetometer. Scientific requirements and measurement approach to detect water/ice to a sensitivity of 50 ppm (hydrogen), measure key elemental constituents, detect radioactive gas release events and accurately map the Moon's gravitational and magnetic fields are given. A brief overview of the programmatic accomplishments in meeting a tightly constrained schedule and budget is also provided.

The Lunar Prospector discovery mission: mission and measurement description.

NASA Astrophysics Data System (ADS)

Hubbard, G. S.; Binder, A. B.; Feldman, W.

Lunar Prospector, the first competitively selected planetary mission in NASA's discovery program, is described with emphasis on the radiation spectrometer instrumentation and anticipated scientific data return. Scheduled to be launched in January 1998, the mission will conduct a one year orbital survey of the moon's composition and structure. The suite of five instruments will be outlined: neutron spectrometer, alpha particle spectrometer, gamma-ray spectrometer, electron reflectometer and magnetometer. Scientific requirements and measurement approach to detect water ice to a sensitivity of 50 ppm (hydrogen), measure key elemental constituents, detect radioactive gas release events and accurately map the moon's gravitational and magnetic fields are given. A brief overview of the programmatic accomplishments in meeting a tightly constrained schedule and budget is also provided.

Fast coarse-fine locating method for φ-OTDR.

PubMed

Mei, Xuanwei; Pang, Fufei; Liu, Huanhuan; Yu, Guoqin; Shao, Yuying; Qian, Tianyu; Mou, Chengbo; Lv, Longbao; Wang, Tingyun

2018-02-05

We proposed and demonstrated a coarse-fine method to achieve fast locating of external vibration for the phase-sensitive optical time-domain reflectometer (φ-OTDR) sensing system. Firstly, the acquired backscattered traces from heterodyne coherent φ-OTDR systems are spatially divided into a few segments along a sensing fiber for coarse locating, and most of the acquired data can be excluded by comparing the phase difference between the endpoints in adjacent segments. Secondly, the amplitude-based locating is implemented within the target segments for fine locating. By using the proposed coarse-fine locating method, we have numerically and experimentally investigated a distributed vibration sensor based on the heterodyne coherent φ-OTDR system with a 50-km-long sensing fiber. We find that the computation cost of signal processing for locating is significantly reduced in the long-haul sensing fiber, showing a potential application in real-time locating of external vibration.

Method and apparatus for probing relative volume fractions

DOEpatents

Jandrasits, Walter G.; Kikta, Thomas J.

1998-01-01

A relative volume fraction probe particularly for use in a multiphase fluid system includes two parallel conductive paths defining therebetween a sample zone within the system. A generating unit generates time varying electrical signals which are inserted into one of the two parallel conductive paths. A time domain reflectometer receives the time varying electrical signals returned by the second of the two parallel conductive paths and, responsive thereto, outputs a curve of impedance versus distance. An analysis unit then calculates the area under the curve, subtracts the calculated area from an area produced when the sample zone consists entirely of material of a first fluid phase, and divides this calculated difference by the difference between an area produced when the sample zone consists entirely of material of the first fluid phase and an area produced when the sample zone consists entirely of material of a second fluid phase. The result is the volume fraction.

Method and apparatus for probing relative volume fractions

DOEpatents

Jandrasits, W.G.; Kikta, T.J.

1998-03-17

A relative volume fraction probe particularly for use in a multiphase fluid system includes two parallel conductive paths defining therebetween a sample zone within the system. A generating unit generates time varying electrical signals which are inserted into one of the two parallel conductive paths. A time domain reflectometer receives the time varying electrical signals returned by the second of the two parallel conductive paths and, responsive thereto, outputs a curve of impedance versus distance. An analysis unit then calculates the area under the curve, subtracts the calculated area from an area produced when the sample zone consists entirely of material of a first fluid phase, and divides this calculated difference by the difference between an area produced when the sample zone consists entirely of material of the first fluid phase and an area produced when the sample zone consists entirely of material of a second fluid phase. The result is the volume fraction. 9 figs.

Distributed Humidity Sensing in PMMA Optical Fibers at 500 nm and 650 nm Wavelengths.

PubMed

Liehr, Sascha; Breithaupt, Mathias; Krebber, Katerina

2017-03-31

Distributed measurement of humidity is a sought-after capability for various fields of application, especially in the civil engineering and structural health monitoring sectors. This article presents a method for distributed humidity sensing along polymethyl methacrylate (PMMA) polymer optical fibers (POFs) by analyzing wavelength-dependent Rayleigh backscattering and attenuation characteristics at 500 nm and 650 nm wavelengths. Spatially resolved humidity sensing is obtained from backscatter traces of a dual-wavelength optical time domain reflectometer (OTDR). Backscatter dependence, attenuation dependence as well as the fiber length change are characterized as functions of relative humidity. Cross-sensitivity effects are discussed and quantified. The evaluation of the humidity-dependent backscatter effects at the two wavelength measurements allows for distributed and unambiguous measurement of relative humidity. The technique can be readily employed with low-cost standard polymer optical fibers and commercial OTDR devices.

Sensitivity of a fibre scattered-light interferometer to external phase perturbations in an optical fibre

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alekseev, A E; Potapov, V T; Gorshkov, B G

2015-10-31

Sensitivity of a fibre scattered-light interferometer to external phase perturbations is studied for the first time. An expression is derived for an average power of a useful signal at the interferometer output under external harmonic perturbations in a signal fibre of the interferometer. It is shown that the maximum sensitivity of the scattered-light interferometer depends on the dispersion of the interferogram intensity. An average signal-to-noise ratio is determined theoretically and experimentally at the output of the interferometer at different amplitudes of external perturbations. Using the measured dependences of the signal-to-noise ratio, the threshold sensitivity of the fibre scattered-light interferometer tomore » external phase perturbations is found. The results obtained can be used to optimise characteristics of optical time-domain reflectometers and to design individual phase-sensitive fibre-optic sensors. (laser applications and other topics in quantum electronics)« less

Multi-point measurement using two-channel reflectometer with antenna switching for study of high-frequency fluctuations in GAMMA 10

NASA Astrophysics Data System (ADS)

Ikezoe, R.; Ichimura, M.; Okada, T.; Itagaki, J.; Hirata, M.; Sumida, S.; Jang, S.; Izumi, K.; Tanaka, A.; Yoshikawa, M.; Kohagura, J.; Sakamoto, M.; Nakashima, Y.

2017-03-01

A two-channel microwave reflectometer system with fast microwave antenna switching capability was developed and applied to the GAMMA 10 tandem mirror device to study high-frequency small-amplitude fluctuations in a hot mirror plasma. The fast switching of the antennas is controlled using PIN diode switches, which offers the significant advantage of reducing the number of high-cost microwave components and digitizers with high bandwidths and large memory that are required to measure the spatiotemporal behavior of the high-frequency fluctuations. The use of two channels rather than one adds the important function of a simultaneous two-point measurement in either the radial direction or the direction of the antenna array to measure the phase profile of the fluctuations along with the normal amplitude profile. The density fluctuations measured using this system clearly showed the high-frequency coherent fluctuations that are associated with Alfvén-ion-cyclotron (AIC) waves in GAMMA 10. A correlation analysis applied to simultaneously measured density fluctuations showed that the phase component that was included in a reflected microwave provided both high coherence and a clear phase difference for the AIC waves, while the amplitude component showed neither significant coherence nor clear phase difference. The axial phase differences of the AIC waves measured inside the hot plasma confirmed the formation of a standing wave structure. The axial variation of the radial profiles was evaluated and a clear difference was found among the AIC waves for the first time, which would be a key to clarify the unknown boundary conditions of the AIC waves.

Direct measurement of density oscillation induced by a radio-frequency wave.

PubMed

Yamada, T; Ejiri, A; Shimada, Y; Oosako, T; Tsujimura, J; Takase, Y; Kasahara, H

2007-08-01

An O-mode reflectometer at a frequency of 25.85 GHz was applied to plasmas heated by the high harmonic fast wave (21 MHz) in the TST-2 spherical tokamak. An oscillation in the phase of the reflected microwave in the rf range was observed directly for the first time. In TST-2, the rf (250 kW) induced density oscillation depends mainly on the poloidal rf electric field, which is estimated to be about 0.2 kV/m rms by the reflectometer measurement. Sideband peaks separated in frequency by ion cyclotron harmonics from 21 MHz, and peaks at ion cyclotron harmonics which are suggested to be quasimodes generated by parametric decay, were detected.

Measurement of two-dimensional thickness of micro-patterned thin film based on image restoration in a spectroscopic imaging reflectometer.

PubMed

Kim, Min-Gab; Kim, Jin-Yong

2018-05-01

In this paper, we introduce a method to overcome the limitation of thickness measurement of a micro-patterned thin film. A spectroscopic imaging reflectometer system that consists of an acousto-optic tunable filter, a charge-coupled-device camera, and a high-magnitude objective lens was proposed, and a stack of multispectral images was generated. To secure improved accuracy and lateral resolution in the reconstruction of a two-dimensional thin film thickness, prior to the analysis of spectral reflectance profiles from each pixel of multispectral images, the image restoration based on an iterative deconvolution algorithm was applied to compensate for image degradation caused by blurring.

AND/R: Advanced neutron diffractometer/reflectometer for investigation of thin films and multilayers for the life sciences

PubMed Central

Dura, Joseph A.; Pierce, Donald J.; Majkrzak, Charles F.; Maliszewskyj, Nicholas C.; McGillivray, Duncan J.; Lösche, Mathias; O'Donovan, Kevin V.; Mihailescu, Mihaela; Perez-Salas, Ursula; Worcester, David L.; White, Stephen H.

2011-01-01

An elastic neutron scattering instrument, the advanced neutron diffractometer/reflectometer (AND/R), has recently been commissioned at the National Institute of Standards and Technology Center for Neutron Research. The AND/R is the centerpiece of the Cold Neutrons for Biology and Technology partnership, which is dedicated to the structural characterization of thin films and multilayers of biological interest. The instrument is capable of measuring both specular and nonspecular reflectivity, as well as crystalline or semicrystalline diffraction at wave-vector transfers up to approximately 2.20 Å−1. A detailed description of this flexible instrument and its performance characteristics in various operating modes are given. PMID:21892232

The multipurpose time-of-flight neutron reflectometer “Platypus” at Australia's OPAL reactor

NASA Astrophysics Data System (ADS)

James, M.; Nelson, A.; Holt, S. A.; Saerbeck, T.; Hamilton, W. A.; Klose, F.

2011-03-01

In this manuscript we describe the major components of the Platypus time-of-flight neutron reflectometer at the 20 MW OPAL reactor in Sydney, Australia. Platypus is a multipurpose spectrometer for the characterisation of solid thin films, materials adsorbed at the solid-liquid interface and free-liquid surfaces. It also has the capacity to study magnetic thin films using spin-polarised neutrons. Platypus utilises a white neutron beam ( λ=2-20 Å) that is pulsed using boron-coated disc chopper pairs; thus providing the capacity to tailor the wavelength resolution of the pulses to suit the system under investigation. Supermirror optical components are used to focus, deflect or spin-polarise the broad bandwidth neutron beams, and typical incident spectra are presented for each configuration. A series of neutron reflectivity datasets are presented, indicating the quality and flexibility of this spectrometer. Minimum reflectivity values of <10 -7 are observed; while maximum thickness values of 325 nm have been measured for single-component films and 483 nm for a multilayer system. Off-specular measurements have also been made to investigate in-plane features as opposed to those normal to the sample surface. Finally, the first published studies conducted using the Platypus time-of-flight neutron reflectometer are presented.

GINA--a polarized neutron reflectometer at the Budapest Neutron Centre.

PubMed

Bottyán, L; Merkel, D G; Nagy, B; Füzi, J; Sajti, Sz; Deák, L; Endrőczi, G; Petrenko, A V; Major, J

2013-01-01

The setup, capabilities, and operation parameters of the neutron reflectometer GINA, the recently installed "Grazing Incidence Neutron Apparatus" at the Budapest Neutron Centre, are introduced. GINA, a dance-floor-type, constant-energy, angle-dispersive reflectometer is equipped with a 2D position-sensitive detector to study specular and off-specular scattering. Wavelength options between 3.2 and 5.7 Å are available for unpolarized and polarized neutrons. Spin polarization and analysis are achieved by magnetized transmission supermirrors and radio-frequency adiabatic spin flippers. As a result of vertical focusing by a five-element pyrolytic graphite monochromator, the reflected intensity from a 20 × 20 mm(2) sample has been doubled. GINA is dedicated to studies of magnetic films and heterostructures, but unpolarized options for non-magnetic films, membranes, and other surfaces are also provided. Shortly after its startup, reflectivity values as low as 3 × 10(-5) have been measured by the instrument. The instrument capabilities are demonstrated by a non-polarized and a polarized reflectivity experiment on a Si wafer and on a magnetic film of [(62)Ni/(nat)Ni](5) isotope-periodic layer composition. The facility is now open for the international user community. Its further development is underway establishing new sample environment options and spin analysis of off-specularly scattered radiation as well as further decreasing the background.

Handheld directional reflectometer: an angular imaging device to measure BRDF and HDR in real time

NASA Astrophysics Data System (ADS)

Mattison, Phillip R.; Dombrowski, Mark S.; Lorenz, James M.; Davis, Keith J.; Mann, Harley C.; Johnson, Philip; Foos, Bryan

1998-10-01

Many applications require quantitative measurements of surface light scattering, including quality control on production lines, inspection of painted surfaces, inspection of field repairs, etc. Instruments for measuring surface scattering typically fall into two main categories, namely bidirectional reflectometers, which measure the angular distribution of scattering, and hemispherical directional reflectometers, which measure the total scattering into the hemisphere above the surface. Measurement of the bi-directional reflectance distribution function (BRDF) gives the greatest insight into how light is scattered from a surface. Measurements of BRDF, however, are typically very lengthy measurements taken by moving a source and detector to map the scattering. Since BRDF has four angular degrees of freedom, such measurements can require hours to days to complete. Instruments for measuring BRDF are also typically laboratory devices, although a field- portable bi-directional reflectometer does exist. Hemispherical directional reflectance (HDR) is a much easier measurement to make, although care must be taken to use the proper methodology when measuring at wavelengths beyond 10 micrometer, since integrating spheres (typically used to make such measurements) are very energy inefficient and lose their integrating properties at very long wavelengths. A few field- portable hemispherical directional reflectometers do exist, but typically measure HDR only at near-normal angles. Boeing Defense and Space Group and Surface Optics Corporation, under a contract from the Air Force Research Laboratory, have developed a new hand-held instrument capable of measuring both BRDF and HDR using a unique, patented angular imaging technique. A combination of an hemi-ellipsoidal mirror and an additional lens translate the angular scatter from a surface into a two-dimensional spatial distribution, which is recorded by an imaging array. This configuration fully maps the scattering from a half-hemisphere above the surface with more than 30,000 angularly-resolved points and update rates to 60 measurements per second. The instrument then computes HDR from the measured BDR. For ease of use, the instrument can also compare both the BRDF and HDR to preset limits, generating a Pass/Fail indicator for HDR and a high-acceptable-low image display of BRDF. Beam incidence elevation is variable from normal incidence ((theta) equals 0 degrees) to 5 degrees off grazing ((theta) equals 85 degrees), while scattering is measured to nearly 90 degrees off normal. Such capability is extremely important for any application requiring knowledge of surface appearance at oblique viewing angles. The current instrument operates over the range of 3 micrometer to 12 micrometer, with extension into the visible band possible.

Lunar Prospector: developing a very low cost planetary mission.

NASA Astrophysics Data System (ADS)

Hubbard, G. S.

Lunar Prospector, the first competitively selected planetary mission in NASA's Discovery Program, is described with emphasis on the lessons learned from managing a very low cost project. Insights into government-industry teaming, project management, contractual arrangements, schedule and budget reserve approach are discussed. The mission is conducting an orbital survey of the Moon's composition and structure. A mission overview and scientific data return is briefly described in the context of low cost mission development. The suite of five instruments is outlined: neutron spectrometer (NS), alpha particle spectrometer (APS), gamma ray spectrometer (GRS), magnetometer (MAG) and an electron reflectometer (ER). Scientific requirements and measurement approaches to detect water ice to a sensitivity of 50 ppm (hydrogen), measure key elemental constituents, detect gas release events and accurately map the Moon's gravitational and magnetic fields are described.

Front-end antenna system design for the ITER low-field-side reflectometer system using GENRAY ray tracing.

PubMed

Wang, G; Doyle, E J; Peebles, W A

2016-11-01

A monostatic antenna array arrangement has been designed for the microwave front-end of the ITER low-field-side reflectometer (LFSR) system. This paper presents details of the antenna coupling coefficient analyses performed using GENRAY, a 3-D ray tracing code, to evaluate the plasma height accommodation capability of such an antenna array design. Utilizing modeled data for the plasma equilibrium and profiles for the ITER baseline and half-field scenarios, a design study was performed for measurement locations varying from the plasma edge to inside the top of the pedestal. A front-end antenna configuration is recommended for the ITER LFSR system based on the results of this coupling analysis.

A simultaneous multiple angle-wavelength dispersive X-ray reflectometer using a bent-twisted polychromator crystal

PubMed Central

Matsushita, Tadashi; Arakawa, Etsuo; Voegeli, Wolfgang; Yano, Yohko F.

2013-01-01

An X-ray reflectometer has been developed, which can simultaneously measure the whole specular X-ray reflectivity curve with no need for rotation of the sample, detector or monochromator crystal during the measurement. A bent-twisted crystal polychromator is used to realise a convergent X-ray beam which has continuously varying energy E (wavelength λ) and glancing angle α to the sample surface as a function of horizontal direction. This convergent beam is reflected in the vertical direction by the sample placed horizontally at the focus and then diverges horizontally and vertically. The normalized intensity distribution of the reflected beam measured downstream of the specimen with a two-dimensional pixel array detector (PILATUS 100K) represents the reflectivity curve. Specular X-ray reflectivity curves were measured from a commercially available silicon (100) wafer, a thin gold film coated on a silicon single-crystal substrate and the surface of liquid ethylene glycol with data collection times of 0.01 to 1000 s using synchrotron radiation from a bending-magnet source of a 6.5 GeV electron storage ring. A typical value of the simultaneously covered range of the momentum transfer was 0.01–0.45 Å−1 for the silicon wafer sample. The potential of this reflectometer for time-resolved X-ray studies of irreversible structural changes is discussed. PMID:23254659

Developments in the realization of diffuse reflectance scales at NPL

NASA Astrophysics Data System (ADS)

Chunnilall, Christopher J.; Clarke, Frank J. J.; Shaw, Michael J.

2005-08-01

The United Kingdom scales for diffuse reflectance are realized using two primary instruments. In the 360 nm to 2.5 μm spectral region the National Reference Reflectometer (NRR) realizes absolute measurement of reflectance and radiance factor by goniometric measurements. Hemispherical reflectance scales are obtained through the spatial integration of these goniometric measurements. In the mid-infrared region (2.5 μm - 55 μm) the hemispherical reflectance scale is realized by the Absolute Hemispherical Reflectometer (AHR). This paper describes some of the uncertainties resulting from errors in aligning the NRR and non-ideality in sample topography, together with its use to carry out measurements in the 1 - 1.6 μm region. The AHR has previously been used with grating spectrometers, and has now been coupled to a Fourier transform spectrometer.

Optical bedside monitoring of cerebral perfusion: technological and methodological advances applied in a study on acute ischemic stroke

NASA Astrophysics Data System (ADS)

Steinkellner, Oliver; Gruber, Clemens; Wabnitz, Heidrun; Jelzow, Alexander; Steinbrink, Jens; Fiebach, Jochen B.; MacDonald, Rainer; Obrig, Hellmuth

2010-11-01

We present results of a clinical study on bedside perfusion monitoring of the human brain by optical bolus tracking. We measure the kinetics of the contrast agent indocyanine green using time-domain near-IR spectroscopy (tdNIRS) in 10 patients suffering from acute unilateral ischemic stroke. In all patients, a delay of the bolus over the affected when compared to the unaffected hemisphere is found (mean: 1.5 s, range: 0.2 s to 5.2 s). A portable time-domain near-IR reflectometer is optimized and approved for clinical studies. Data analysis based on statistical moments of time-of-flight distributions of diffusely reflected photons enables high sensitivity to intracerebral changes in bolus kinetics. Since the second centralized moment, variance, is preferentially sensitive to deep absorption changes, it provides a suitable representation of the cerebral signals relevant for perfusion monitoring in stroke. We show that variance-based bolus tracking is also less susceptible to motion artifacts, which often occur in severely affected patients. We present data that clearly manifest the applicability of the tdNIRS approach to assess cerebral perfusion in acute stroke patients at the bedside. This may be of high relevance to its introduction as a monitoring tool on stroke units.

φ-OTDR sensing system with bidirectional pumped fiber Raman amplifier and unbalanced MZ interferometer

NASA Astrophysics Data System (ADS)

Zhang, Liang; Tian, Ming; Dong, Lei

2017-10-01

In order to improve the detection distance and the sensitivity, we propose a novel distributed optical fiber sensing system. This system is composed of bidirectional pumping fiber Raman amplifier and unbalanced fiber Mach-Zehnder interferometer. Based on the interference mechanism of phase sensitive optical time domain reflectometer (φ-OTDR), the system can get the sensing information of the whole optical fiber by analyzing the backward scattered light. The interferometer is used as the demodulator of the sensing system, which consists of a 3×3 coupler and two faraday rotator mirrors. By means of the demodulator, the signal light is divided into three beams with fixed phase difference. To deal with these three signals, we can get the vibration information directly on the optical fiber. Through experimental study, this system has a high sensitivity. The maximum sensing length and the spatial resolution of the φ-OTDR system are 100 km and 10 m. The signal to noise ratio about 18 dB is achieved.

Design and Test of an Event Detector for the ReflectoActive Seals System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stinson, Brad J

2006-05-01

The purpose of this thesis was to research, design, develop and test a novel instrument for detecting fiber optic loop continuity and spatially locating fiber optic breaches. The work is for an active seal system called ReflectoActive Seals whose purpose is to provide real time container tamper indication. A Field Programmable Gate Array was used to implement a loop continuity detector and a spatial breach locator based on a high acquisition speed single photon counting optical time domain reflectometer. Communication and other control features were added in order to create a usable instrument that met defined requirements. A host graphicalmore » user interface was developed to illustrate system use and performance. The resulting device meets performance specifications by exhibiting a dynamic range of 27dB and a spatial resolution of 1.5 ft. The communication scheme used expands installation options and allows the device to communicate to a central host via existing Local Area Networks and/or the Internet.« less

Design and Test of an Event Detector and Locator for the ReflectoActive Seals System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stinson, Brad J

2006-06-01

The purpose of this work was to research, design, develop and test a novel instrument for detecting fiber optic loop continuity and spatially locating fiber optic breaches. The work is for an active seal system called ReflectoActive{trademark} Seals whose purpose is to provide real time container tamper indication. A Field Programmable Gate Array was used to implement a loop continuity detector and a spatial breach locator based on a high acquisition speed single photon counting optical time domain reflectometer. Communication and other control features were added in order to create a usable instrument that met defined requirements. A host graphicalmore » user interface was developed to illustrate system use and performance. The resulting device meets performance specifications by exhibiting a dynamic range of 27dB and a spatial resolution of 1.5 ft. The communication scheme used expands installation options and allows the device to communicate to a central host via existing Local Area Networks and/or the Internet.« less

Method and apparatus for probing relative volume fractions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jandrasits, W.G.; Kikta, T.J.

1996-12-31

A relative volume fraction probe particularly for use in a multiphase fluid system includes two parallel conductive paths defining there between a sample zone within the system. A generating unit generates time varying electrical signals which are inserted into one of the two parallel conductive paths. A time domain reflectometer receives the time varying electrical signals returned by the second of the two parallel conductive paths and, responsive thereto, outputs a curve of impedance versus distance. An analysis unit then calculates the area under the curve, subtracts the calculated area from an area produced when the sample zone consists entirelymore » of material of a first fluid phase, and divides this calculated difference by the difference between an area produced when the sample zone consists entirely of material of the first fluid phase and an area produced when the sample zone consists entirely of material of a second fluid phase. The result is the volume fraction.« less

Distributed transverse stress measurement along an optic fiber using polarimetric OFDR.

PubMed

Wei, Changjiang; Chen, Hongxin; Chen, Xiaojun; Chen, David; Li, Zhihong; Yao, X Steve

2016-06-15

We report a novel polarimetric optical frequency domain reflectometer (P-OFDR) that can simultaneously measure both space-resolved transverse stresses and light back-reflections along an optic fiber with sub-mm spatial resolution. By inducing transversal stresses and optical back-reflections at multiple points along a length of optic fiber, we demonstrate that our system can unambiguously distinguish the stresses from the back-reflections of a fiber with a fiber length longer than 800 m, a spatial resolution of 0.5 mm, a maximum stress level of up to 200 kpsi (1379 Mpa), a minimum stress of about 10 kpsi (69 Mpa), and a stress measurement uncertainty of 10%. We show that our P-OFDR can clearly identify the locations and magnitudes of the stresses inside a fiber coil induced during a fiber winding process. The P-OFDR can be used for fiber health monitoring for critical fiber links, fiber gyro coil characterization, and other distributed fiber sensing applications.

Structural health monitoring of IACC yachts using fiber optic distributed strain sensors: a technical challenge for America's Cup 2000

NASA Astrophysics Data System (ADS)

Murayama, Hideaki; Kageyama, Kazuro; Kimpara, Isao; Akiyoshi, Shimada; Naruse, Hiroshi

2000-06-01

In this study, we developed a health monitoring system using a fiber optic distributed strain sensor for International America's Cup Class (IACC) yachts. Most structural components of an IACC yacht consist of an aluminum honeycomb core sandwiched between carbon fiber reinforced plastic (CFRP) laminates. In such structures, delamination, skin/core debonding and debonding between adhered members will be result in serious fracture of the structure. We equipped two IACC yachts with fiber optic strain sensors designed to measured the distributed strain using a Brillouin optical time domain reflectometer (BOTDR) and to detect any deterioration or damage to the yacht's structures caused by such failures. And based on laboratory test results, we proposed a structural health monitoring technique for IACC yachts that involves analyzing their strain distribution. Some important information about structural conditions of the IACC yachts could be obtained from this system through the periodical strain measurements in the field.

Novel mono-static arrangement of the ASDEX Upgrade high field side reflectometers compatible with electron cyclotron resonance heating stray radiation.

PubMed

Silva, A; Varela, P; Meneses, L; Manso, M

2012-10-01

The ASDEX Upgrade frequency modulated continuous wave broadband reflectometer system uses a mono-static antenna configuration with in-vessel hog-horns and 3 dB directional couplers. The operation of the new electron cyclotron resonance heating (ECRH) launcher and the start of collective Thomson scattering experiments caused several events where the fragile dummy loads inside the high field side directional couplers were damaged, due to excessive power resulting from the ECRH stray fields. In this paper, we present a non-conventional application of the existing three-port directional coupler that hardens the system to the ECRH stray fields and at the same time generates the necessary reference signal. Electromagnetic simulations and laboratory tests were performed to validate the proposed solution and are compared with the in-vessel calibration tests.

Invited Article: Polarization ``Down Under'': The polarized time-of-flight neutron reflectometer PLATYPUS

NASA Astrophysics Data System (ADS)

Saerbeck, T.; Klose, F.; Le Brun, A. P.; Füzi, J.; Brule, A.; Nelson, A.; Holt, S. A.; James, M.

2012-08-01

This review presents the implementation and full characterization of the polarization equipment of the time-of-flight neutron reflectometer PLATYPUS at the Australian Nuclear Science and Technology Organisation (ANSTO). The functionality and efficiency of individual components are evaluated and found to maintain a high neutron beam polarization with a maximum of 99.3% through polarizing Fe/Si supermirrors. Neutron spin-flippers with efficiencies of 99.7% give full control over the incident and scattered neutron spin direction over the whole wavelength spectrum available in the instrument. The first scientific experiments illustrate data correction mechanisms for finite polarizations and reveal an extraordinarily high reproducibility for measuring magnetic thin film samples. The setup is now fully commissioned and available for users through the neutron beam proposal system of the Bragg Institute at ANSTO.

Invited article: polarization "down under": the polarized time-of-flight neutron reflectometer PLATYPUS.

PubMed

Saerbeck, T; Klose, F; Le Brun, A P; Füzi, J; Brule, A; Nelson, A; Holt, S A; James, M

2012-08-01

This review presents the implementation and full characterization of the polarization equipment of the time-of-flight neutron reflectometer PLATYPUS at the Australian Nuclear Science and Technology Organisation (ANSTO). The functionality and efficiency of individual components are evaluated and found to maintain a high neutron beam polarization with a maximum of 99.3% through polarizing Fe/Si supermirrors. Neutron spin-flippers with efficiencies of 99.7% give full control over the incident and scattered neutron spin direction over the whole wavelength spectrum available in the instrument. The first scientific experiments illustrate data correction mechanisms for finite polarizations and reveal an extraordinarily high reproducibility for measuring magnetic thin film samples. The setup is now fully commissioned and available for users through the neutron beam proposal system of the Bragg Institute at ANSTO.

Intensity noise limit in a phase-sensitive optical time-domain reflectometer with a semiconductor laser source

NASA Astrophysics Data System (ADS)

E Alekseev, A.; Tezadov, Ya A.; Potapov, V. T.

2017-05-01

In the present paper we perform, for the first time, the analysis of the average intensity noise power level at the output of a coherent phase-sensitive optical time-domain reflectometer (phase-OTDR) with a semiconductor laser source. The origin of the considered intensity noise lies in random phase fluctuations of a semiconductor laser source field. These phase fluctuations are converted to intensity noise in the process of interference of backscattered light. This intensity noise inevitably emerges in every phase-OTDR spatial channel and limits its sensitivity to external phase actions. The analysis of intensity noise in a phase-OTDR was based on the study of a fiber scattered-light interferometer (FSLI) which is treated as the constituent part of OTDR. When considered independently, FSLI has a broad intensity noise spectrum at its output; when FSLI is treated as a part of a phase-OTDR, due to aliasing effect, the wide FSLI noise spectrum is folded within the spectral band, determined by the probe pulse repetition frequency. In the analysis one of the conventional phase-OTDR schemes with rectangular dual-pulse probe signal was considered, the FSLI, which corresponds to this OTDR scheme, has two scattering fiber segments with additional time delay introduced between backscattered fields. The average intensity noise power and resulting noise spectrum at the output of this FSLI are determined by the degree of coherence of the semiconductor laser source, the length of the scattering fiber segments and by the additional time delay between the scattering segments. The average intensity noise characteristics at the output of the corresponding phase-OTDR are determined by the analogous parameters: the source coherence, the lengths of the parts constituting the dual-pulse and the time interval which separates the parts of the dual-pulse. In the paper the expression for the average noise power spectral density (NPSD) at the output of FSLI was theoretically derived and experimentally verified. Based on the found average NPSD of FSLI, a simple relation connecting the phase-OTDR parameters and the limiting level of full average intensity noise power at its output was derived. This relation was verified by experimental measurement of the average noise power at the output of phase-OTDR. The limiting noise level, considered in the paper, determines the fundamental noise floor for the phase-OTDR with given parameters of the source coherence, probe pulse length and time delay between two pulses constituting the dual-pulse.

Sensitivity of a phase-sensitive optical time-domain reflectometer with a semiconductor laser source

NASA Astrophysics Data System (ADS)

Alekseev, A. E.; Tezadov, Ya A.; Potapov, V. T.

2018-06-01

In the present paper we perform, for the first time, an analysis of the average sensitivity of a coherent phase-sensitive optical time-domain reflectometer (phase-OTDR) with a semiconductor laser source to external actions. The sensitivity of this OTDR can be defined in a conventional manner via average SNR at its output, which in turn is defined by the average useful signal power and the average intensity noise power in the OTDR spatial channels in the bandwidth defined by the OTDR sampling frequency. The average intensity noise power is considered in detail in a previous paper. In the current paper we examine the average useful signal power at the output of a phase-OTDR. The analysis of the average useful signal power of a phase-OTDR is based on the study of a fiber scattered-light interferometer (FSLI) which is treated as a constituent part of a phase- OTDR. In the analysis, one of the conventional phase-OTDR schemes with a rectangular dual-pulse probe signal is considered. The FSLI which corresponds to this OTDR scheme has two scattering fiber segments with additional time delay, introduced between backscattered fields. The average useful signal power and the resulting average SNR at the output of this FSLI are determined by the degree of coherence of the semiconductor laser source, the length of the scattering fiber segments, and by the additional time delay between the scattering fiber segments. The average useful signal power characteristic of the corresponding phase-OTDR is determined by analogous parameters: the source coherence, the time durations of the parts constituting the dual-pulse, and the time interval which separates these parts. In the paper an expression for the average useful signal power of a phase-OTDR is theoretically derived and experimentally verified. Based on the found average useful signal power of a phase-OTDR and the average intensity noise power, derived in the previous paper, the average SNR of a phase-OTDR is defined. Setting the average signal SNR to 1, at a defined spectral band the minimum detectable external action amplitude for our particular phase-OTDR setup is determined. We also derive a simple relation for the average useful signal power and the average SNR which results when making the assumption that the laser source coherence is high. The results of the paper can serve as the basis for further development of the concept of phase-OTDR sensitivity.

Passive Wireless Vibration Sensing for Measuring Aerospace Structural Flutter

NASA Technical Reports Server (NTRS)

Wilson, William C.; Moore, Jason P.

2017-01-01

To reduce energy consumption, emissions, and noise, NASA is exploring the use of high aspect ratio wings on subsonic aircraft. Because high aspect ratio wings are susceptible to flutter events, NASA is also investigating methods of flutter detection and suppression. In support of that work a new remote, non-contact method for measuring flutter-induced vibrations has been developed. The new sensing scheme utilizes a microwave reflectometer to monitor the reflected response from an aeroelastic structure to ultimately characterize structural vibrations. To demonstrate the ability of microwaves to detect flutter vibrations, a carbon fiber-reinforced polymer (CFRP) composite panel was vibrated at various frequencies from 1Hz to 130Hz. The reflectometer response was found to closely resemble the sinusoidal response as measured with an accelerometer up to 100 Hz. The data presented demonstrate that microwaves can be used to measure flutter-induced aircraft vibrations.

Reflectometer for pseudo-Brewster angle spectrometry (BAIRS)

NASA Astrophysics Data System (ADS)

Potter, Roy F.

2000-10-01

A simple, robust reflectometer, pre-set for several angles of incidence (AOI), has been designed and used for determining the optical parameters of opaque samples having a specular surface. A single, linear polarizing element permits the measurement of perpendicular(s) and parallel (p) reflectence at each AOI. The BAIRS algorithm determines the empirical optical parameters for the subject surface at the pseudo-Brewster AOI, based on the measurement of p/s at two AOI's and, in turn the optical constants n and k (or (epsilon) 1 and (epsilon) 2). Radiation sources in current use, are a stabilized tungsten-halide lamp or a deuterium lamp for the visible and near UV spectral regions. Silica fiber optics and lenses deliver input and output radiation from the source and to a CCD array scanned diffraction spectrometer. Results for a sample of GaAs will be presented along with a discussion of dispersion features in the optical constant spectra.

Photoconductive circuit element reflectometer

DOEpatents

Rauscher, Christen

1990-01-01

A photoconductive reflectometer for characterizing semiconductor devices at millimeter wavelength frequencies where a first photoconductive circuit element (PCE) is biased by a direct current voltage source and produces short electrical pulses when excited into conductance by short first laser light pulses. The electrical pulses are electronically conditioned to improve the frequency related amplitude characteristics of the pulses which thereafter propagate along a transmission line to a device under test. Second PCEs are connected along the transmission line to sample the signals on the transmission line when excited into conductance by short second laser light pulses, spaced apart in time a variable period from the first laser light pulses. Electronic filters connected to each of the second PCEs act as low-pass filters and remove parasitic interference from the sampled signals and output the sampled signals in the form of slowed-motion images of the signals on the transmission line.

Photoconductive circuit element reflectometer

DOEpatents

Rauscher, C.

1987-12-07

A photoconductive reflectometer for characterizing semiconductor devices at millimeter wavelength frequencies where a first photoconductive circuit element (PCE) is biased by a direct current voltage source and produces short electrical pulses when excited into conductance by short first laser light pulses. The electrical pulses are electronically conditioned to improve the frequency related amplitude characteristics of the pulses which thereafter propagate along a transmission line to a device under test. Second PCEs are connected along the transmission line to sample the signals on the transmission line when excited into conductance by short second laser light pulses, spaced apart in time a determinable period from the first laser light pulses. Electronic filters connected to each of the second PCEs act as low-pass filters and remove parasitic interference from the sampled signals and output the sampled signals in the form of slowed-motion images of the signals on the transmission line. 4 figs.

A Computer Aided Broad Band Impedance Matching Technique Using a Comparison Reflectometer. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Gordy, R. S.

1972-01-01

An improved broadband impedance matching technique was developed. The technique is capable of resolving points in the waveguide which generate reflected energy. A version of the comparison reflectometer was developed and fabricated to determine the mean amplitude of the reflection coefficient excited at points in the guide as a function of distance, and the complex reflection coefficient of a specific discontinuity in the guide as a function of frequency. An impedance matching computer program was developed which is capable of impedance matching the characteristics of each disturbance independent of other reflections in the guide. The characteristics of four standard matching elements were compiled, and their associated curves of reflection coefficient and shunt susceptance as a function of frequency are presented. It is concluded that an economical, fast, and reliable impedance matching technique has been established which can provide broadband impedance matches.

New signal processing technique for density profile reconstruction using reflectometry.

PubMed

Clairet, F; Ricaud, B; Briolle, F; Heuraux, S; Bottereau, C

2011-08-01

Reflectometry profile measurement requires an accurate determination of the plasma reflected signal. Along with a good resolution and a high signal to noise ratio of the phase measurement, adequate data analysis is required. A new data processing based on time-frequency tomographic representation is used. It provides a clearer separation between multiple components and improves isolation of the relevant signals. In this paper, this data processing technique is applied to two sets of signals coming from two different reflectometer devices used on the Tore Supra tokamak. For the standard density profile reflectometry, it improves the initialization process and its reliability, providing a more accurate profile determination in the far scrape-off layer with density measurements as low as 10(16) m(-1). For a second reflectometer, which provides measurements in front of a lower hybrid launcher, this method improves the separation of the relevant plasma signal from multi-reflection processes due to the proximity of the plasma.

Reflectometry diagnostics on TCV

NASA Astrophysics Data System (ADS)

Molina Cabrera, Pedro; Coda, Stefano; Porte, Laurie; Offeddu, Nicola; Tcv Team

2017-10-01

Both profile reflectometer and Doppler back-scattering (DBS) diagnostics are being developed for the TCV Tokamak using a steerable quasi-optical launcher and universal polarizers. First results will be presented. A pulse reflectometer is being developed to complement Thomson Scattering measurements of electron density, greatly increasing temporal resolution and also effectively enabling fluctuation measurements. Pulse reflectometry consists of sending short pulses of varying frequency and measuring the roundtrip group-delay with precise chronometers. A fast arbitrary waveform generator is used as a pulse source feeding frequency multipliers that bring the pulses to V-band. A DBS diagnostic is currently operational in TCV. DBS may be used to infer the perpendicular velocity and wave number spectrum of electron density fluctuations in the 3-15 cm-1 wave-number range. Off-the-shelf transceiver modules, originally used for VNA measurements, are being used in a Doppler radar configuration. See author list of S. Coda et al., 2017 Nucl. Fusion 57 102011.

Effect of Various Finishing Procedures on the Reflectivity (Shine) of Tooth Enamel - An In-vitro Study.

PubMed

Patil, Harshal Ashok; Chitko, Shrikant Shrinivas; Kerudi, Veerendra Virupaxappa; Maheshwari, Amit Ratanlal; Patil, Neeraj Suresh; Tekale, Pawankumar Dnyandeo; Gore, Ketan Ashorao; Zope, Amit Ashok

2016-08-01

Reflectivity of an object is a good parameter for surface finish. As the patient evaluates finishing as a function of gloss/reflectivity/shine an attempt is made here to evaluate changes in surface finish with custom made reflectometer. The aim of the present study was to study the effect of various procedures during orthodontic treatment on the shine of enamel, using a custom made reflectometer. Sixty one extracted premolars were collected and each tooth was mounted on acrylic block. Reflectivity of the teeth was measured as compared to standard before any procedure. One tooth was kept as standard throughout the study. Sixty teeth were acid etched. Reflectivity was measured on custom made reflectometer and readings recorded. Same procedure was repeated after debonding. Then 60 samples were divided into three groups: Group 1 - Tungsten Carbide, Group 2 - Astropol, Group 3- Sof-Lex disc depending upon the finishing method after debonding and reflectivity was measured. The mean percentage of reflectivity after acid etching was 31.4%, debonding 45.5%, Tungsten carbide bur finishing (Group 1) was 58.3%, Astropol (Group 2) 72.8%, and Sof-Lex disc (Group 3) 84.4% as that to the standard. There was statistically very highly significant (p<0.001) difference in reflectivity restored by the three finishing materials in the study. Thus, the light reflection was better in Group 3> Group 2> Group 1. The primary goal was to restore the enamel to its original state after orthodontic treatment. The methods tested in this study could not restore the original enamel reflectivity.

Investigation clogging dynamic of permeable pavement systems using embedded sensors

NASA Astrophysics Data System (ADS)

Razzaghmanesh, Mostafa; Borst, Michael

2018-02-01

Permeable pavement is a stormwater control measure commonly selected in both new and retrofit applications. However, there is limited information about the clogging mechanism of these systems that effects the infiltration. A permeable pavement site located at the Seitz Elementary School, on Fort Riley, Kansas was selected for this study. An 80-space parking lot was built behind the school as part of an EPA collaboration with the U.S. Army. The parking lot design includes a permeable interlocking concrete pavement section along the downgradient edge. This study monitored the clogging progress of the pavement section using twelve water content reflectometers and three buried tipping bucket rain gauges. This clogging dynamic investigation was divided into three stages namely pre-clogged, transitional, and clogged. Recorded initial relative water content of all three stages were significantly and negatively correlated to antecedent dry weather periods with stronger correlations during clogged conditions. The peak relative water content correlation with peak rainfall 10-min intensity was significant for the water content reflectometers located on the western edge away from the eastern edge; this correlation was strongest during transition stage. Once clogged, rainfall measurements no longer correlated with the buried tipping bucket rain gauges. Both water content reflectometers and buried tipping bucket rain gauges showed the progress of surface clogging. For every 6 mm of rain, clogging advanced 1 mm across the surface. The results generally support the hypothesis that the clogging progresses from the upgradient to the downgradient edge. The magnitude of the contributing drainage area and rainfall characteristics are effective factors on rate and progression of clogging.

Radiometric Calibration Techniques for Signal-of-Opportunity Reflectometers

NASA Technical Reports Server (NTRS)

Piepmeier, Jeffrey R.; Shah, Rashmi; Deshpande, Manohar; Johnson, Carey

2014-01-01

Bi-static reflection measurements utilizing global navigation satellite service (GNSS) or other signals of opportunity (SoOp) can be used to sense ocean and terrestrial surface properties. End-to-end calibration of GNSS-R has been performed using well-characterized reflection surface (e.g., water), direct path antenna, and receiver gain characterization. We propose an augmented approach using on-board receiver electronics for radiometric calibration of SoOp reflectometers utilizing direct and reflected signal receiving antennas. The method calibrates receiver and correlator gains and offsets utilizing a reference switch and common noise source. On-board electronic calibration sources, such as reference switches, noise diodes and loop-back circuits, have shown great utility in stabilizing total power and correlation microwave radiometer and scatterometer receiver electronics in L-band spaceborne instruments. Application to SoOp instruments is likely to bring several benefits. For example, application to provide short and long time scale calibration stability of the direct path channel, especially in low signal-to-noise ratio configurations, is directly analogous to the microwave radiometer problem. The direct path channel is analogous to the loopback path in a scatterometer to provide a reference of the transmitted power, although the receiver is independent from the reflected path channel. Thus, a common noise source can be used to measure the gain ratio of the two paths. Using these techniques long-term (days to weeks) calibration stability of spaceborne L-band scatterometer and radiometer has been achieved better than 0.1. Similar long-term stability would likely be needed for a spaceborne reflectometer mission to measure terrestrial properties such as soil moisture.

78 FR 46932 - Notice of Availability of Government-Owned Inventions; Available for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-02

... APPARATUS, Issued on June 18, 2013//U.S. Patent Number 8,477,308: POLARIZED, SPECULAR REFLECTOMETER APPARATUS, Issued on July 2, 2013. ADDRESSES: Requests for copies of the inventions cited should be directed...

Coincident Retrieval of Ocean Surface Roughness and Salinity Using Airborne and Satellite Microwave Radiometry and Reflectometry Measurements during the Carolina Offshore (Caro) Experiment.

NASA Astrophysics Data System (ADS)

Burrage, D. M.; Wesson, J. C.; Wang, D. W.; Garrison, J. L.; Zhang, H.

2017-12-01

The launch of the Cyclone Global Navigation Satellite System (CYGNSS) constellation of 8 microsats carrying GPS L-band reflectometers on 15 Dec., 2016, and continued operation of the L-band radiometer on the European Space Agency (ESA) Soil Moisture and Ocean Salinity (SMOS) satellite, allow these complementary technologies to coincidentally retrieve Ocean surface roughness (Mean Square Slope, MSS), Surface Wind speed (WSP), and Sea Surface Salinity (SSS). The Carolina Offshore (Caro) airborne experiment was conducted jointly by NRL SSC and Purdue University from 7-11 May, 2017 with the goal of under-flying CYGNSS and SMOS and overflying NOAA buoys, to obtain high-resolution reflectometer and radiometer data for combined retrieval of MSS, SSS and WSP on the continental shelf. Airborne instruments included NRL's Salinity Temperature and Roughness Remote Scanner (STARRS) L-, C- and IR-band radiometer system, and a 4-channel dual-pol L-band (GPS) and S-band (XM radio) reflectometer, built by Purdue University. Flights either crossed NOAA buoys on various headings, or intersected with specular point ground tracks at predicted CYGNSS overpass times. Prevailing winds during Caro were light to moderate (1-8 m/s), so specular returns dominated the reflectometer Delay Doppler Maps (DDMs), and MSS was generally low. In contrast, stronger winds (1-12 m/s) and rougher seas (wave heights 1-5 m) were experienced during the preceding Maine Offshore (Maineo) experiment in March, 2016. Several DDM observables were used to retrieve MSS and WSP, and radiometer brightness temperatures produced Sea Surface Temperature (SST), SSS and also WSP estimates. The complementary relationship of Kirchoff's formula e+r=1, between radiometric emissivity, e, and reflectivity, r, was exploited to seek consistent estimates of MSS, and use it to correct the SSS retrievals for sea surface roughness effects. The relative performance and utility of the various airborne and satellite retrieval algorithms were assessed, and the coincident buoy, aircraft and satellite retrievals of MSS, WSP and SSS were compared. During Caro WSP from the different instruments generally agreed. Some anomalously high wind retrievals found here and elsewhere in current CYGNSS Level 2 data may yield to the science team's recent L1 calibration revision.

Effect of parameters in moving average method for event detection enhancement using phase sensitive OTDR

NASA Astrophysics Data System (ADS)

Kwon, Yong-Seok; Naeem, Khurram; Jeon, Min Yong; Kwon, Il-bum

2017-04-01

We analyze the relations of parameters in moving average method to enhance the event detectability of phase sensitive optical time domain reflectometer (OTDR). If the external events have unique frequency of vibration, then the control parameters of moving average method should be optimized in order to detect these events efficiently. A phase sensitive OTDR was implemented by a pulsed light source, which is composed of a laser diode, a semiconductor optical amplifier, an erbium-doped fiber amplifier, a fiber Bragg grating filter, and a light receiving part, which has a photo-detector and high speed data acquisition system. The moving average method is operated with the control parameters: total number of raw traces, M, number of averaged traces, N, and step size of moving, n. The raw traces are obtained by the phase sensitive OTDR with sound signals generated by a speaker. Using these trace data, the relation of the control parameters is analyzed. In the result, if the event signal has one frequency, then the optimal values of N, n are existed to detect the event efficiently.

Real-time monitoring and fault locating using amplified spontaneous emission noise reflection for tree-structured Ethernet passive optical networks

NASA Astrophysics Data System (ADS)

Naim, Nani Fadzlina; Ab-Rahman, Mohammad Syuhaimi; Kamaruddin, Nur Hasiba; Bakar, Ahmad Ashrif A.

2013-09-01

Nowadays, optical networks are becoming dense while detecting faulty branches in the tree-structured networks has become problematic. Conventional methods are inconvenient as they require an engineer to visit the failure site to check the optical fiber using an optical time-domain reflectometer. An innovative monitoring technique for tree-structured network topology in Ethernet passive optical networks (EPONs) by using the erbium-doped fiber amplifier to amplify the traffic signal is demonstrated, and in the meantime, a residual amplified spontaneous emission spectrum is used as the input signal to monitor the optical cable from the central office. Fiber Bragg gratings with distinct center wavelengths are employed to reflect the monitoring signals. Faulty branches of the tree-structured EPONs can be identified using a simple and low-cost receiver. We will show that this technique is capable of providing monitoring range up to 32 optical network units using a power meter with a sensitivity of -65 dBm while maintaining the bit error rate of 10-13.

Effect of inflow discharges on the development of matric suction and volumetric water content for dike during overtopping tests

NASA Astrophysics Data System (ADS)

Hassan, Marwan A.; Ismail, Mohd A. M.

2017-10-01

The point of this review is to depict the impact of various inflow discharge rate releases on the instruments of matric suction and volumetric water content during an experimental test of spatial overtopping failure at school of civil engineering in universiti Sains of Malaysia. A dry sand dike was conducted inside small flume channel with twelve sensors of tensiometer and Time-Domain Reflectometer (TDR). Instruments are installed in the soil at different locations in downstream and upstream slopes of the dike for measuring the response of matric suction and volumetric water content, respectively. Two values of inflow discharge rates of 30 and 40 L/min are utilized as a part of these experiments to simulate the effectiveness of water reservoirs in erosion mechanism. The outcomes demonstrate that the matric suction and volumetric water content are decreased and increased, respectively for both inflow discharges. The higher inflow discharges accelerate the saturation of dike soil and the erosion process faster than that for the lower inflow discharges.

Durability tests of a fiber optic corrosion sensor.

PubMed

Wan, Kai Tai; Leung, Christopher K Y

2012-01-01

Steel corrosion is a major cause of degradation in reinforced concrete structures, and there is a need to develop cost-effective methods to detect the initiation of corrosion in such structures. This paper presents a low cost, easy to use fiber optic corrosion sensor for practical application. Thin iron film is deposited on the end surface of a cleaved optical fiber by sputtering. When light is sent into the fiber, most of it is reflected by the coating. If the surrounding environment is corrosive, the film is corroded and the intensity of the reflected signal drops significantly. In previous work, the sensing principle was verified by various experiments in laboratory and a packaging method was introduced. In this paper, the method of multiplexing several sensors by optical time domain reflectometer (OTDR) and optical splitter is introduced, together with the interpretation of OTDR results. The practical applicability of the proposed sensors is demonstrated in a three-year field trial with the sensors installed in an aggressive marine environment. The durability of the sensor against chemical degradation and physical degradation is also verified by accelerated life test and freeze-thaw cycling test, respectively.

Role of superconducting electronics in advancing science and technology (invited) (abstract)

NASA Astrophysics Data System (ADS)

Faris, S. M.

1988-08-01

The promises of the ultrahigh-performance properties of superconductivity and Josephson junction technologies have been known for quite some time. This presentation describes the first superconducting electronics and measurement system and its important role as a major tool to advance microwave and millimeter wave technologies. This breakthrough tool is a sampling oscilloscope with 5-ps rise time, 50-μV sensitivity, and a time domain reflectometer with 8-ps rise time. In order to achieve these performance goals, several technological hurdles had to be overcome including perfecting a manufacturing process for building Josephson junction IC chips, developing an innovative cooling technique, developing interfaces and interconnections with bandwidths in excess of 70 GHz, and developing the room-temperature hardware and software necessary to make the instruments convenient, easy to use, easy to learn, in addition to making available functions and features users have come to expect from sophisticated digital test instrumentation. These technological developments are stepping stones leading to the realization of more sophisticated and complex electronic systems satisfying the needs of scientists, technologists, and engineers. The unprecedented speed and sensitivity make it possible to attack new frontiers.

A novel reflectometer for relative reflectance measurements of CCDs

NASA Astrophysics Data System (ADS)

Hart, Murdock; Barkhouser, Robert H.; Gunn, James E.; Smee, Stephen A.

2016-07-01

The high quantum efficiencies (QE) of backside illuminated charge coupled devices (CCD) has ushered in the age of the large scale astronomical survey. The QE of these devices can be greater than 90%, and is dependent upon the operating temperature, device thickness, backside charging mechanisms, and anti-reflection (AR) coatings. But at optical wavelengths the QE is well approximated as one minus the reflectance, thus the measurement of the backside reflectivity of these devices provides a second independent measure of their QE. We have designed and constructed a novel instrument to measure the relative specular reflectance of CCD detectors, with a significant portion of this device being constructed using a 3D fused deposition model (FDM) printer. This device implements both a monitor and measurement photodiode to simultaneously collect in- cident and reflected measurements reducing errors introduced by the relative reflectance calibration process. While most relative reflectometers are highly dependent upon a precisely repeatable target distance for accurate measurements, we have implemented a method of measurement which minimizes these errors. Using the reflectometer we have measured the reflectance of two types of Hamamatsu CCD detectors. The first device is a Hamamatsu 2k x 4k backside illuminated high resistivity p-type silicon detector which has been optimized to operate in the blue from 380 nm - 650 nm. The second detector being a 2k x 4k backside illuminated high resistivity p-type silicon detector optimized for use in the red from 640 nm - 960 nm. We have not only been able to measure the reflectance of these devices as a function of wavelength we have also sampled the reflectance as a function of position on the device, and found a reflection gradient across these devices.

On-farm quick tests for estimating nitrogen in dairy manure.

PubMed

Van Kessel, J S; Reeves, J B

2000-08-01

Manure nutrient analyses performed rapidly on the farm could be useful for nutrient management programs. The objective of this experiment was to evaluate six quick tests for their accuracy in estimating total manure N or NH4+-N. The quick tests included the hydrometer, electrical conductivity meter and pen, reflectometer, Agros N Meter, and Quantofix-N-Volumeter. The hydrometer was used to estimate total N, while the remaining tests were used to estimate NH4+-N. Samples (107) were collected from dairy farms in five northeastern states. Samples were analyzed for total N and NH4+-N by traditional laboratory methods and using each of the quick tests. Manure compositions ranged from 1.4 to 38.6% dry matter (DM), 0.9 to 9.5 kg/m3 total N, and 0.3 to 4.7 kg/m3 NH4+-N. The estimated concentration of total N or NH4+-N determined by each quick test was regressed against laboratory-determined values. The hydrometer did not estimate total N accurately. The strongest relationship for estimation of NH4+-N was with the Quantofix-N-Volumeter followed by the Agros N Meter, the reflectometer, and the electrical conductivity meter and pen. When the samples were split into high (>12%) and low (< or =12%) DM groups, in all cases the r2 for the regression equation was higher for the low DM group than for the high DM group. The Agros N Meter, the reflectometer, and the conductivity meter and pen did not perform well for the high DM group. These data indicate that several quick tests are viable options for measuring NH4+-N concentrations in dairy slurries and solids.

SPEAR — ToF neutron reflectometer at the Los Alamos Neutron Science Center

NASA Astrophysics Data System (ADS)

Dubey, M.; Jablin, M. S.; Wang, P.; Mocko, M.; Majewski, J.

2011-11-01

This article discusses the Surface ProfilE Analysis Reflectometer (SPEAR), a vertical scattering geometry time-of-flight reflectometer, at the Los Alamos National Laboratory Lujan Neutron Scattering Center. SPEAR occupies flight path 9 and receives spallation neutrons from a polychromatic, pulsed (20Hz) source that pass through a liquid-hydrogen moderator at 20K coupled with a Be filter to shift their energy spectrum. The spallation neutrons are generated by bombarding a tungsten target with 800MeV protons obtained from an accelerator. The process produces an integrated neutron flux of ˜ 3.4×106 cm-2 s-1 at a proton current of 100 μA. SPEAR employs choppers and frame overlap mirrors to obtain a neutron wavelength range of 4.5-16 Å. SPEAR uses a single 200mm long 3He linear position-sensitive detector with ˜ 2 mm FWHM resolution for simultaneous studies of both specular and off-specular scattering. SPEAR's moderated neutrons are collimated into a beam which impinges from above upon a level sample with an average angle of 0.9° to the horizontal, to facilitate air-liquid interface studies. In the vertical direction, the beam converges at the sample position. The neutrons can be further collimated to the desired divergence by finely slitting the beam using a set of two 10B4C slit packages. The instrument is ideally suited to study organic and inorganic thin films with total thicknesses between 5 and 3000 Å in a variety of environments. Specifically designed sample chambers available at the instrument provide the opportunity to study biological systems at the solid-liquid interface. SPEAR's unique experimental capabilities are demonstrated by specific examples in this article. Finally, an outlook for SPEAR and perspectives on future instrumentation are discussed.

Apparatus for Teaching Physics.

ERIC Educational Resources Information Center

Gottlieb, Herbert H., Ed.

1982-01-01

Discusses: (1) construction of an integrated spherical reflectometer; (2) limitations of the NOAA Weather Radio Network; and (3) a simple experiment to demonstrate/measure influence of damping force on amplitude resonance. Also discusses whether or not a homemade electrophorus can lose its charge and then recharge itself. (JN)

A low cost, simple, portable instrument for the measurement of infra-red reflectance of paints

NASA Astrophysics Data System (ADS)

Marson, F.

1982-05-01

The construction and design of a low cost, simple, portable infra-red reflectometer which can be used to estimate the reflectance of paint films in the 800 nm region is described. The infra-red reflectances of a range of lustreless, semigloss and gloss olive drab camouflage paints determined using this instrument are compared to those obtained using modified commercial equipment and to the reflectances measured at 800 nm using a Cary model 17 spectrophotometer. The new reflectometer was shown to be superior to the modified commercial instrument currently specified in Australian government paint specifications and to be capable of estimating the reflectance of olive drab paints to within about one per cent of the Cary derived reflectance values. The reflectance values for a range of 24 experimental coatings made with pigments of varying absorption in the infra-red region are used to illustrate the effect of the instrument's spectral response and the necessity of establishing a reliable working standard.

Implementation of the new multichannel X-mode edge density profile reflectometer for the ICRF antenna on ASDEX Upgrade

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aguiam, D. E., E-mail: daguiam@ipfn.tecnico.ulisboa.pt; Silva, A.; Carvalho, P. J.

A new multichannel frequency modulated continuous-wave reflectometry diagnostic has been successfully installed and commissioned on ASDEX Upgrade to measure the plasma edge electron density profile evolution in front of the Ion Cyclotron Range of Frequencies (ICRF) antenna. The design of the new three-strap ICRF antenna integrates ten pairs (sending and receiving) of microwave reflectometry antennas. The multichannel reflectometer can use three of these to measure the edge electron density profiles up to 2 × 10{sup 19} m{sup −3}, at different poloidal locations, allowing the direct study of the local plasma layers in front of the ICRF antenna. ICRF power coupling,more » operational effects, and poloidal variations of the plasma density profile can be consistently studied for the first time. In this work the diagnostic hardware architecture is described and the obtained density profile measurements were used to track outer radial plasma position and plasma shape.« less

Technical overview of the millimeter-wave imaging reflectometer on the DIII-D tokamak (invited)

DOE PAGES

Muscatello, Christopher M.; Domier, Calvin W.; Hu, Xing; ...

2014-07-22

The two-dimensional mm-wave imaging reflectometer (MIR) on DIII-D is a multi-faceted device for diagnosing electron density fluctuations in fusion plasmas. Its multi-channel, multi-frequency capabilities and high sensitivity permit visualization and quantitative diagnosis of density perturbations, including correlation length, wavenumber, mode propagation velocity, and dispersion. The two-dimensional capabilities of MIR are made possible with twelve vertically separated sightlines and four-frequency operation (corresponding to four radial channels). The 48-channel DIII-D MIR system has a tunable source that can be stepped in 500 µs increments over a range of 56 to 74 GHz. An innovative optical design keeps both on-axis and off-axis channelsmore » focused at the cutoff surface, permitting imaging over an extended poloidal region. As a result, the integrity of the MIR optical design is confirmed by comparing Gaussian beam calculations to laboratory measurements of the transmitter beam pattern and receiver antenna patterns.« less

Millimeter-wave reflectometry for electron density profile and fluctuation measurements on NSTX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kubota, S.; Nguyen, X. V.; Peebles, W. A.

2001-01-01

A millimeter-wave reflectometry system for electron density profile and fluctuation measurements is being developed and installed on the National Spherical Torus Experiment. The initial frequency coverage will be in the bands 12--18, 20--32, and 33--50 GHz, provided by frequency-tunable solid-state sources. These frequencies correspond to O-mode cutoff densities ranging from 1.8x10{sup 12} to 3.1x10{sup 13}cm{sup -3}, which will span both the plasma core ({rho}=r/a<0.8) and edge ({rho}>0.8) regions. Operated as a broadband swept-frequency (frequency-modulated continuous-wave) reflectometer, the diagnostic is expected to provide routine (shot-to-shot) time- ({<=}50 {mu}s) and spatially resolved ({approx}1 cm) density profiles. The previous hardware can be easilymore » reconfigured as a fixed-frequency reflectometer for density fluctuation measurements. The combination of measurements would be valuable for studying phenomena such as possible L- to H-mode transitions and edge-localized modes.« less

High Resolution Millimeter Wave Detection of Vertical Cracks in the Space Shuttle External Tank Spray-On-Foam Insulation (SOFI)

NASA Technical Reports Server (NTRS)

Kharkovsky, S.; Zoughi, R.; Hepburn, F.

2006-01-01

Space Shuttle Columbia s catastrophic failure, the separation of a piece of spray-on-foam insulation (SOFI) from the external tank (ET) in the Space Shuttle Discovery s flight in 2005 and crack detected in its ET foam prior to its successful launch in 2006 emphasize the need for effective nondestructive methods for inspecting the shuttle ET SOFI. Millimeter wave nondestructive testing methods have been considered as potential and effective inspection tools for evaluating the integrity of the SOFI. This paper presents recent results of an investigation for the purpose of detecting vertical cracks in SOFI panels using a focused millimeter wave (150 GHz) reflectometer. The presented images of the SOFI panels show the capability of this reflectometer for detecting tight vertical cracks (also as a function of crack opening dimension) in exposed SOFI panels and while covered by a piece of SOFI ramp simulating a more realistic and challenging situation.

Comparison of a 3-D GPU-Assisted Maxwell Code and Ray Tracing for Reflectometry on ITER

NASA Astrophysics Data System (ADS)

Gady, Sarah; Kubota, Shigeyuki; Johnson, Irena

2015-11-01

Electromagnetic wave propagation and scattering in magnetized plasmas are important diagnostics for high temperature plasmas. 1-D and 2-D full-wave codes are standard tools for measurements of the electron density profile and fluctuations; however, ray tracing results have shown that beam propagation in tokamak plasmas is inherently a 3-D problem. The GPU-Assisted Maxwell Code utilizes the FDTD (Finite-Difference Time-Domain) method for solving the Maxwell equations with the cold plasma approximation in a 3-D geometry. Parallel processing with GPGPU (General-Purpose computing on Graphics Processing Units) is used to accelerate the computation. Previously, we reported on initial comparisons of the code results to 1-D numerical and analytical solutions, where the size of the computational grid was limited by the on-board memory of the GPU. In the current study, this limitation is overcome by using domain decomposition and an additional GPU. As a practical application, this code is used to study the current design of the ITER Low Field Side Reflectometer (LSFR) for the Equatorial Port Plug 11 (EPP11). A detailed examination of Gaussian beam propagation in the ITER edge plasma will be presented, as well as comparisons with ray tracing. This work was made possible by funding from the Department of Energy for the Summer Undergraduate Laboratory Internship (SULI) program. This work is supported by the US DOE Contract No.DE-AC02-09CH11466 and DE-FG02-99-ER54527.

Lunar Prospector: First Results and Lessons Learned

NASA Astrophysics Data System (ADS)

Scott Hubbard, G.; Feldman, William; Cox, Sylvia A.; Smith, Marcie A.; Chu-Thielbar, Lisa

2002-01-01

Lunar Prospector, the first competitively selected mission in NASA's Discovery Program, is conducting a one-year orbital survey of the Moon's composition and structure. Launched on January 6 1998, the suite of five instruments is measuring water/ice to a sensitivity of 50 ppm (hydrogen), detecting key elemental constituents, gas release events and mapping the Moon's gravitational and magnetic fields. The mission is described with emphasis on the first scientific results and lessons learned from managing a very low cost project. A mission overview and systems description is given along with final mission trajectories. Lessons learned from government-industry teaming, new modes of project management, and novel contractual arrangements are discussed. The suite of five instruments (neutron spectrometer, alpha particle spectrometer, gamma-ray spectrometer, electron reflectometer and magnetometer) is outlined with attention to final technical performance as well as development on a constrained budget and schedule. A review of our novel approaches to education and public outreach is discussed and a summary with suggestions and implications for future missions is provided.

Use of Water Content Reflectometers in Bioinfiltration/Bioretention to Measure Water Movement and Estimate Evapotranspiration - abstract

EPA Science Inventory

Most bioinfiltration/bioretention models assume runoff is evenly distributed across the surface area and after the engineered fill media is no longer saturated, the volumetric water content (VWC) is constant throughout the media profile and at field capacity. Four to nine water ...

Use of Water Content Reflectometers in Bioinfiltration/Bioretention to Measure Water Movement and Estimate Evapotranspiration

EPA Science Inventory

Most bioinfiltration/bioretention models assume runoff is evenly distributed across the surface area and after the engineered fill media is no longer saturated, the volumetric water content (VWC) is constant throughout the media profile and at field capacity. Four to nine water ...

BioRef: A versatile time-of-flight reflectometer for soft matter applications at Helmholtz-Zentrum Berlin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strobl, M.; Kreuzer, M.; Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin

2011-05-15

BioRef is a versatile novel time-of-flight reflectometer featuring a sample environment for in situ infrared spectroscopy at the reactor neutron source BER II of the Helmholtz Zentrum Berlin fuer Materialien und Energie (HZB). After two years of design and construction phase the instrument has recently undergone commissioning and is now available for specular and off-specular neutron reflectivity measurements. BioRef is especially dedicated to the investigation of soft matter systems and studies at the solid-liquid interface. Due to flexible resolution modes and variable addressable wavelength bands that allow for focusing onto a selected scattering vector range, BioRef enables a broad rangemore » of surface and interface investigations and even kinetic studies with subsecond time resolution. The instrumental settings can be tailored to the specific requirements of a wide range of applications. The performance is demonstrated by several reference measurements, and the unique option of in situ on-board infrared spectroscopy is illustrated by the example of a phase transition study in a lipid multilayer film.« less

Scrape-off layer reflectometer for Alcator C-Mod.

PubMed

Lau, Cornwall; Hanson, Greg; Wilgen, John; Lin, Yijun; Wukitch, Steve

2010-10-01

A swept-frequency X-mode reflectometer is being built for Alcator C-Mod to measure the scrape-off layer density profiles at the top, middle, and bottom locations in front of both the new lower hybrid launcher and the new ion cyclotron range of frequencies antenna. The system is planned to operate between 100 and 146 GHz at sweep rates from 10 μs to 1 ms, and will cover a density range of approximately 10(16)-10(20) m(-3) at B(0)=5-5.4 T. To minimize the effects of density fluctuations, both differential phase and full phase reflectometry will be employed. Design, test data, and calibration results of this electronics system will be discussed. To reduce attenuation losses, tallguide (TE(01)) will be used for most of the transmission line system. Simulations of high mode conversion in tallguide components, such as e-plane hyperbolic secant radius of curvature bends, tapers, and horn antennas will be shown. Experimental measurements of the total attenuation losses of these components in the lower hybrid waveguide run will also be presented.

Complex EUV imaging reflectometry: spatially resolved 3D composition determination and dopant profiling with a tabletop 13nm source

NASA Astrophysics Data System (ADS)

Porter, Christina L.; Tanksalvala, Michael; Gerrity, Michael; Miley, Galen P.; Esashi, Yuka; Horiguchi, Naoto; Zhang, Xiaoshi; Bevis, Charles S.; Karl, Robert; Johnsen, Peter; Adams, Daniel E.; Kapteyn, Henry C.; Murnane, Margaret M.

2018-03-01

With increasingly 3D devices becoming the norm, there is a growing need in the semiconductor industry and in materials science for high spatial resolution, non-destructive metrology techniques capable of determining depth-dependent composition information on devices. We present a solution to this problem using ptychographic coherent diffractive imaging (CDI) implemented using a commercially available, tabletop 13 nm source. We present the design, simulations, and preliminary results from our new complex EUV imaging reflectometer, which uses coherent 13 nm light produced by tabletop high harmonic generation. This tool is capable of determining spatially-resolved composition vs. depth profiles for samples by recording ptychographic images at multiple incidence angles. By harnessing phase measurements, we can locally and nondestructively determine quantities such as device and thin film layer thicknesses, surface roughness, interface quality, and dopant concentration profiles. Using this advanced imaging reflectometer, we can quantitatively characterize materials-sciencerelevant and industry-relevant nanostructures for a wide variety of applications, spanning from defect and overlay metrology to the development and optimization of nano-enhanced thermoelectric or spintronic devices.

Experimental investigation of RC beams using BOTDA(R)-FRP-OF

NASA Astrophysics Data System (ADS)

Zhou, Zhi; He, Jianping; Huang, Ying; Ou, Jinping

2008-04-01

Brillouin based fiber optic sensing turns to be a promising technology for Structural Health Monitoring (SHM). However, the bare optical fiber is too fragile to act as a practical sensor, so high durability and large range (large strain) Brillouin distributed sensors are in great needs in field applications. For this reason, high durable and large range optical fiber Brillouin Optical Time Domain Analysis (Reflectometer) sensors packaged by Fiber Reinforcement Polymer (FRP), named BOTDA(R)-FRP-OF, have been studied and developed. Besides, in order to study the large strain, crack and slip between the rebar and concrete in reinforced concrete (RC) beams using BOTDR(A) technique, five RC Beams installed with BOTDA(R)-FRP-OF sensors have been set up. And the damage characteristics of the RC beams were investigated by comparing the strain measured by the BOTDA(R)-FRP-OF sensors and the strain from traditional electric strain gauges and Fiber Bragg Grating (FBG) sensors, respectively. The test results show that the BOTDA(R)-FRP-OF sensor can effectively detect the damage (including crack and slip) characteristic of RC beam, and it is suitable for the long-term structural health monitoring on concrete structures such as bridge, big dam and so on.

Massive gas insufflation without effect on esophageal reflectometry profiles

NASA Astrophysics Data System (ADS)

Raphael, David T.; Arnaudov, Dimiter; Benbassat, Maxim

2003-10-01

Time-domain acoustic reflectometry generates a ``one-dimensional'' image of the interior of a cavity in the form of an area-distance profile. After patient intubation with a breathing tube, the characteristic reflectometry profile consists of a constant-area segment corresponding to the length of the tube, followed either by a rapid increase in the area beyond the carina (lung) or by a sudden decrease in the area to zero (esophagus). In the cardiac arrest setting, during mistaken placement of the breathing tube into the esophagus, followed by aggressive manual ventilation, is it possible to markedly distend the esophagus, such that the esophageal profile looks like a tracheal profile? With approval of the USC IUCAC Committee, an animal study was conducted with anesthetized, tracheally intubated, and mechanically ventilated dogs. With a separate breathing tube in the esophagus, aggressive esophageal ventilation (comparable to that seen in the cardiopulmonary resuscitation setting) was accomplished with a manual resuscitation bag. A Benson Hood Labs two-microphone reflectometer was used to obtain esophageal profiles with and without the above ventilation. In this pilot study, there was no significant esophageal distention as a result of the above ventilation. [Research supported by the Alfred E. Mann Institute.

OTDR fiber-optical chemical sensor system for detection and location of hydrocarbon leakage.

PubMed

Buerck, J; Roth, S; Kraemer, K; Mathieu, H

2003-08-15

A distributed sensing system for apolar hydrocarbons is presented which is built from a polymer-clad silica fiber adapted to an optical time domain reflectometer (OTDR) set-up. OTDR measurements allow locating and detecting chemicals by measuring the time delay between short light pulses entering the fiber and discrete changes in the backscatter signals that are caused by local extraction of hydrocarbons into the fiber cladding. The light guiding properties of the fiber are affected by interaction of the extracted chemicals with the evanescent wave light field extending into the fiber cladding. Distributed sensing of pure liquid hydrocarbons (HC) and aqueous HC solutions with a commercially available mini-OTDR adapted to sensing fibers of up to 1km length could be demonstrated. A pulsed laser diode emitting at the 850 nm telecommunication wavelength was applied in the mini-OTDR to locate the HCs by analyzing the step drop (light loss) in the backscatter signal, which is induced by local refractive index (RI) increase in the silicone cladding due to the extracted HC. The prototype instrument can be applied for monitoring hydrocarbon leakage in large technical installations, such as tanks, chemical pipelines or chemical waste disposal containments.

Design considerations for high-power VHF radar transceivers: Phase matching long coaxial cables using a cable radar

NASA Technical Reports Server (NTRS)

Johnson, P. E.; Ecklund, W. L.

1983-01-01

The Poker Flat 49.92-MHz MST radar uses 64 phase-controlled transmitters in individual shelters distributed throughout the antenna array. Phase control is accomplished by sampling the transmitted pulse at the directional coupler of each transmitter and sending the sample pulse back to a phase-control unit. This method requires phase matching 64 long (256 meter) coaxial cables (RG-213) to within several electrical degrees. Tests with a time domain reflectometer showed that attenuation of high frequency components in the long RG-213 cable rounded the leading edge of the reflected pulse so that the cables could only be measured to within 50 cm (about 45 deg at 49.92 MHz). Another measurement technique using a vector voltmeter to compare forward and reflected phase required a directional coupler with unattainable directivity. Several other techniques were also found lacking, primarily because of loss in the long RG-213 cables. At this point it was realized that what was needed was a simple version of the phase-coherent clear-air radar, i.e., a cable radar. The design and operation of this cable are described.

Effects of low Earth orbit environment on the Long Duration Exposure Facility thermal control coatings

NASA Technical Reports Server (NTRS)

Sampair, Thomas R.; Berrios, William M.

1992-01-01

One of the benefits of the Long Duration Exposure Facility (LDEF) was the opportunity to study the before and after effects of low earth orbit space environment on the spacecraft thermal control coatings. Since the LDEF's thermal control was totally passive by design, the selection of the external surface absorptivity to emissivity ratio (alpha/epsilon) and the ability for the coating to retain the alpha/epsilon over time was an important consideration in the thermal design of the LDEF. The primary surface coating chosen for the LDEF structure was clear chromic anodized aluminum with an average design alpha/epsilon of 0.32/0.16. External surface absorptivity (alpha) and emissivity (epsilon) were measured on all intercostals, longerons, tray mounting flanges, thermal control panels, and a limited number of experiment surface coatings after the experiment trays were removed from the LDEF structure. All surface alpha/epsilon measurements were made using portable hand held infrared and solar spectrum reflectometers. The absorptivity measurements were taken with a Devices and Services SSR-ER version 5.0 solar spectra reflectometer which has a stated uncertainty of +/- 0.01, and all normal emissivity measurements were made using the Gier Dunkle DB-100 infrared reflectometer also with a stated uncertainty of +/- 0.01. Both instruments were calibrated in the laboratory by LaRC instrumentation personnel before being used in the field at KSC. A combined total of 733 measurements were taken on the anodized aluminum hardware which included the structure (intercostals, longerons, and center ring), earth and space end thermal control panels, and experiment tray mounting flanges. The facility thermal control coatings measured in this survey cover 33 percent of the total exposed LDEF surface area. To correlate low earth orbit environmental effects on the anodized coatings, measurements were taken in both exposed and unexposed surfaces and compared to quality assurance (QA) measurements taken on the new surfaces at the time of hardware fabrication in 1978. The results of investigation are presented.

An evaluation of the NASA/GSFC Barnes field spectral reflectometer model 14-758, using signal/noise as a measure of utility

NASA Astrophysics Data System (ADS)

Bell, R.; Labovitz, M. L.

1982-07-01

A Barnes field spectral reflectometer which collected information in 373 channels covering the region from 0.4 to 2.5 micrometers was assessed for signal utility. A band was judged unsatisfactory if the probability was 0.1 or greater than its signal to noise ratio was less than eight to one. For each of the bands the probability of a noisy observation was estimated under a binomial assumption from a set of field crop spectra covering an entire growing season. A 95% confidence interval was calculated about each estimate and bands whose lower confidence limits were greater than 0.1 were judged unacceptable. As a result, 283 channels were deemed statistically satisfactory. Excluded channels correspond to portions of the electromagnetic spectrum (EMS) where high atmospheric absorption and filter wheel overlap occur. In addition, the analyses uncovered intervals of unsatisfactory detection capability within the blue, red and far infrared regions of vegetation spectra. From the results of the analysis it was recommended that 90 channels monitored by the instrument under consideration be eliminated from future studies. These channels are tabulated and discussed.

AMOR - the versatile reflectometer at SINQ

NASA Astrophysics Data System (ADS)

Clemens, D.; Gross, P.; Keller, P.; Schlumpf, N.; Könnecke, M.

2000-03-01

We report on a new facility for neutron reflectometry situated at the end position of a cold neutron guide at the Swiss Spallation Neutron Source SINQ. The instrument is a flexible apparatus, adaptable to the needs of the user's individual experiment. Principally designed to operate in the time-of-flight mode it is also capable to exploit the fact that SINQ is a continuous source because PSI's developments in the field of thin film multilayers are fruitfully applied. By means of multilayer monochromators it can be converted into a constant wavelength reflectometer. Polarized neutron reflectometry on AMOR takes advantage of remanent FeCo/Ti:N supermirrors and multilayers which can be operated in a way that no spin flippers are needed. The time and angular contributions to the resolution in momentum transfer are separately determinable in TOF mode. The total length of the instrument is adjustable in order to optimize resolution together with the illumination of the sample's surface. Large sample environments can be placed on the sample table that is actively isolated against vibrations. Single detectors and an EMBL 3He area detector can be chosen, alternatively. The instrument concept as well as parameters of its components are presented.

A simple solution to systematic errors in density determination by X-ray reflectivity: The XRR-density evaluation (XRR-DE) method

NASA Astrophysics Data System (ADS)

Bergese, P.; Bontempi, E.; Depero, L. E.

2006-10-01

X-ray reflectivity (XRR) is a non-destructive, accurate and fast technique for evaluating film density. Indeed, sample-goniometer alignment is a critical experimental factor and the overriding error source in XRR density determination. With commercial single-wavelength X-ray reflectometers, alignment is difficult to control and strongly depends on the operator. In the present work, the contribution of misalignment on density evaluation error is discussed, and a novel procedure (named XRR-density evaluation or XRR-DE method) to minimize the problem will be presented. The method allows to overcome the alignment step through the extrapolation of the correct density value from appropriate non-specular XRR data sets. This procedure is operator independent and suitable for commercial single-wavelength X-ray reflectometers. To test the XRR-DE method, single crystals of TiO 2 and SrTiO 3 were used. In both cases the determined densities differed from the nominal ones less than 5.5%. Thus, the XRR-DE method can be successfully applied to evaluate the density of thin films for which only optical reflectivity is today used. The advantage is that this method can be considered thickness independent.

Portable Chemical Agent Detection System: Differential Reflectometer and Light Scattering Approaches

DTIC Science & Technology

2005-02-15

possible to conduct elemental analysis on modified capillaries because of the polymer coating. Instead, measurements of electroosmotic flow were used...design There are several essential requirements for a sensitive chemiluminescence cell (Figure 1); good reagent/analyte mixing for maximum photon yield...Cutaway of Chemiluminescence cell the cooled pint housing. In our design, the concentric inlets will increase photon collection due to better mixing of

Distributed Fiber Optic Sensor for On-Line Monitoring of Coal Gasifier Refractory Health

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Anbo; Yu, Zhihao

This report summarizes technical progress on the program “Distributed Fiber Optic Sensor for On-Line Monitoring of Coal Gasifier Refractory Health,” funded by the National Energy Technology Laboratory of the U.S. Department of Energy, and performed by the Center for Photonics Technology of the Bradley Department of Electrical and Computer Engineering at Virginia Tech. The scope of work entails analyses of traveling grating generation technologies in an optical fiber, as well as the interrogation of the gratings to infer a distributed temperature along the fiber, for the purpose of developing a real-time refractory health condition monitoring technology for coal gasifiers. Duringmore » the project period, which is from 2011-2015, three different sensing principles were studied, including four-wave mixing (FWM), coherent optical time-domain reflectometer (C-OTDR) and Brillouin optical time-domain analysis (BOTDA). By comparing the three methods, the BOTDA was selected for further development into a complete bench-top sensing system for the proposed high-temperature sensing application. Based on the input from Eastman Chemical, the industrial collaborator on this project, a cylindrical furnace was designed and constructed to simulate typical gasifier refractory temperature conditions in the laboratory, and verify the sensor’s capability to fully monitor refractory conditions on the back-side at temperatures up to 1000°C. In the later stages of the project, the sensing system was tested in the simulated environment for its sensing performance and high-temperature survivability. Through theoretical analyses and experimental research on the different factors affecting the sensor performance, a sensor field deployment strategy was proposed for possible future sensor field implementations.« less

Geomorphic, hydrologic, and erosion data for selected reclaimed hillslopes, the Seneca II Mine, Routt County, Colorado, October 1988 - July 1990

USGS Publications Warehouse

Elliott, J.G.

1993-01-01

Geomorphic, hydrologic, and erosion data were collected from five reclaimed hillslopes at the Seneca II mine near Hayden, Colorado. Hillslope surveys were used to determine hillslope lengths, which range from 670 to 1,280 ft, and hillslope gradients, which range from 0.17 to 0.23 ft/ft (17 to 23 percent). Elevations in the study area range from 6,890 to 7,140 feet and hillslope aspect generally is west or south. Mean total vegetation cover ranges from 74 to 91 percent. Total monthly precipitation for December 1988 through May 1990 was computed from daily measurements made with weighing-bucket precipitation gages. Several snowpack measurements were made during 2 winters. Volumetric soil-water content was determined at incremental depths using a neutron probe and in the upper 11.8 in of soil using a time-domain reflectometer. Active and recent soil erosion was indicated by the presence of rills. Rill density (the sum of rill lengths/unit area) was computed at 50-feet intervals along each hillslope study area. Differences in soil-surface elevations between September or October 1989 and June 1990 were determined with an erosion frame and replicate soil-surface surveys at 16 erosion-study plots.

Cistern Performance for Stormwater Management in Camden ...

EPA Pesticide Factsheets

The Camden County Municipal Utilities Authority (CCMUA) installed different types of green infrastructure Stormwater Control Measures (SCMs) at locations around the city of Camden, NJ. The installed SCMs include cisterns. Cisterns provide a cost effective approach to reduce stormwater runoff volume and peak discharge. The collected water can be used as a substitute for potable water in some applications. This presentation focuses on five cisterns that were monitored as part of a capture and use system at community gardens. The cisterns capture water from existing rooftops or shade structures installed by CCMUA as part of the project. Cistern volumes varied from 305 gallons to 1100 gallons based on the available roof area. Water level was monitored at 10-minute intervals using pressure transducers and rainfall was recorded using tipping bucket rain gauges. Soil moisture was monitored near the root zone using frequency domain reflectometer buried under selected plants. These data were analyzed to better understand the supply and demand relationship. Cisterns were sampled at 6 to 8 week intervals through the growing season for determination of microorganism, nutrients and metal concentrations. The analyses detected Antimony, Arsenic, Barium, Copper, Lead, Manganese, Nickel, Vanadium and Zinc. Concentration of all these metals were below recommended water quality criteria for irrigation by EPA guideline for water reuse. The total nitrogen and phosphorous concen

Optical Fiber Distributed Sensing Structural Health Monitoring (SHM) Strain Measurements Taken During Cryotank Y-Joint Test Article Load Cycling at Liquid Helium Temperatures

NASA Technical Reports Server (NTRS)

Allison, Sidney G.; Prosser, William H.; Hare, David A.; Moore, Thomas C.; Kenner, Winfred S.

2007-01-01

This paper outlines cryogenic Y-joint testing at Langley Research Center (LaRC) to validate the performance of optical fiber Bragg grating strain sensors for measuring strain at liquid helium temperature (-240 C). This testing also verified survivability of fiber sensors after experiencing 10 thermal cool-down, warm-up cycles and 400 limit load cycles. Graphite composite skins bonded to a honeycomb substrate in a sandwich configuration comprised the Y-joint specimens. To enable SHM of composite cryotanks for consideration to future spacecraft, a light-weight, durable monitoring technology is needed. The fiber optic distributed Bragg grating strain sensing system developed at LaRC is a viable substitute for conventional strain gauges which are not practical for SHM. This distributed sensing technology uses an Optical Frequency Domain Reflectometer (OFDR). This measurement approach has the advantage that it can measure hundreds of Bragg grating sensors per fiber and the sensors are all written at one frequency, greatly simplifying fiber manufacturing. Fiber optic strain measurements compared well to conventional strain gauge measurements obtained during these tests. These results demonstrated a high potential for a successful implementation of a SHM system incorporating LaRC's fiber optic sensing system on the composite cryotank and other future cryogenic applications.

Cistern and planter box monitoring in Camden, NJ revisited ...

EPA Pesticide Factsheets

The Camden County Municipal Utilities Authority installed green infrastructure Stormwater Control Measures at multiple locations around the city of Camden, NJ. The Stormwater Control Measures include raised downspout planter boxes and cisterns. EPA is monitoring a subset of the locations to document the performance of individual Stormwater Control Measures. The selected monitoring sites include two sets of raised downspout planter boxes and five cisterns. These Stormwater Control Measures are being monitored: to investigate their hydrologic performances, to document water consumption patterns of cisterns for a better understanding of the supply and demand relationship, and to analyze cistern water quality. The continuous electronic monitoring devices included time domain reflectometers, rain gauges and pressure transducers. EPA decided to monitor these Stormwater Control Measures for three years and second year monitoring is ongoing. Monitoring data present the internal water flow patterns and media saturation frequency of the raised planter boxes and the capture ratio, water use patterns and water quality analysis of cisterns. Second year monitoring shows larger capture ratio for cisterns compared to the first year data and higher metal concentration at one site. The high metal concentration was later resolved by flushing the cistern and resampling. The presentation will summarize the comparison between first and second year data, providing results from the

Microwave Imaging Radar Reflectometer System Utilizing Digital Beam Forming

NASA Astrophysics Data System (ADS)

Hu, Fengqi; Li, Meijiao; Domier, Calvin W.; Liu, Xiaoguang; Luhmann, Neville C., Jr.

2016-10-01

Microwave Imaging Reflectometry is a radar-like technique developed to measure the electron density fluctuations in fusion plasmas. Phased Antenna Arrays can serve as electronically controlled ``lenses'' that can generate the required wavefronts by phase shifting and amplitude scaling, which is being realized in the digital domain with higher flexibility and faster processing speed. In the transmitter, the resolution of the phase control is 1.4 degrees and the amplitude control is 0.5 dB/ step. A V-band double-sided, printed bow tie antenna which exhibits 49% bandwidth (46 - 76 GHz) is employed. The antenna is fed by a microstrip transmission line for easy impedance matching. The simple structure and the small antenna are suitable for low cost fabrication, easy circuit integration, and phased antenna array multi-frequency applications. In the receiver part, a sub-array of 32 channels with 200 mil spacing is used to collect the scattered reflected signal from one unit spot on the plasma cutoff surface. Pre-amplification is used to control the noise level of the system and wire bondable components are used to accommodate the small spacing between each channel. After down converting, base band signals are digitized and processed in an FPGA module. U.S. Department of Energy Grant No. DE-FG02-99ER54531.

Pressure-Water Content Relations for a Sandy, Granitic Soil Under Field and Laboratory Conditions

NASA Astrophysics Data System (ADS)

Chandler, D. G.; McNamara, J. M.; Gribb, M. M.

2001-12-01

A new sensor was developed to measure soil water potential in order to determine the predominant mechanisms of snowmelt delivery to streamflow. The sensors were calibrated for +50 to -300 cm for application on steep granitic slopes and deployed at three depths and 2 locations on a slope in a headwater catchment of the Idaho Batholith throughout the 2001 snowmelt season. Soil moisture was measured simultaneously with Water Content Reflectometers (Cambell Scientific, Logan, UT), that were calibrated in situ with Time Domain Reflectometry measurements. Sensor performance was evaluated in a laboratory soil column via side-by-side monitoring during injection of water with a cone permeameter. Soil characteristic curves were also determined for the field site by multi-step outflow tests. Comparison of the results from the field study to those from the laboratory experiment and to the characteristic curves demonstrate the utility of the new sensor for recording dynamic changes in soil water status. During snowmelt, the sensor responded to both matric potential and bypass-flow pore potential. Large shifts in the pressure record that correspond to changes in the infiltration flux indicate initiation and cessation of macropore flow. The pore pressure records may be used to document the frequency, timing and duration of bypass flow that are not apparent from the soil moisture records.

Refractive-index profiling of embedded microstructures in optical materials

NASA Astrophysics Data System (ADS)

Dave, Digant P.; Milner, Thomas E.

2002-04-01

We describe use of a phase-sensitive low-coherence reflectometer to measure spatial variation of refractive index in optical materials. The described interferometric technique is demonstrated to be a valuable tool to profile the refractive index of optical elements such as integrated waveguides and photowritten optical microstructures. As an example, a refractive-index profile is mapped of a microstructure written in a microscope glass slide with an ultrashort-pulse laser.

OPTICAL FIBRES AND FIBREOPTIC SENSORS: Polarisation reflectometry of anisotropic optical fibres

NASA Astrophysics Data System (ADS)

Konstantinov, Yurii A.; Kryukov, Igor'I.; Pervadchuk, Vladimir P.; Toroshin, Andrei Yu

2009-11-01

Anisotropic, polarisation-maintaining fibres have been studied using a reflectometer and integrated optic polariser. Linearly polarised pulses were launched into the fibre under test at different angles between their plane of polarisation and the main optical axis of the fibre. A special procedure for the correlation analysis of these reflectograms is developed to enhance the reliability of the information about the longitudinal optical uniformity ofanisotropic fibres.

Development of Long-Pulse Heating and Current Drive Actuators and Operational Techniques Compatible with a High-Z Divertor and First Wall

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Guiding

Accurate measurement of the edge electron density profile is essential to optimizing antenna coupling and assessment of impurity contamination in studying long-pulse plasma heating and current drive in fusion devices. Measurement of the edge density profile has been demonstrated on the US fusion devices such as C-Mod, DIII-D, and TFTR amongst many devices, and has been used for RF loading and impurity modeling calculations for many years. University of Science and Technology of China (USTC) has recently installed a density profile reflectometer system on the EAST fusion device at the Institute of Plasma Physics, Chinese Academy of Sciences in Chinamore » based on the University of California Los Angeles (UCLA)-designed reflectometer system on the DIII-D fusion device at General Atomics Company in San Diego, California. UCLA has been working with USTC to optimize the existing microwave antenna, waveguide system, microwave electronics, and data analysis to produce reliable edge density profiles. During the past budget year, progress has been made in all three major areas: effort to achieve reliable system operations under various EAST operational conditions, effort to optimize system performance, and effort to provide quality density profiles into EAST’s database routinely.« less

Prototype Development and Evaluation of Self-Cleaning Concentrated Solar Power Collectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mazumder, Malay K.; Horenstein, Mark N.; Joglekar, Nitin R.

The feasibility of integrating and retrofitting transparent electrodynamic screens (EDS) on the front surfaces of solar collectors was established as a means to provide active self-cleaning properties for parabolic trough and heliostat reflectors, solar panels, and Fresnel lenses. Prototype EDS-integrated solar collectors, including second-surface glass mirrors, metallized Acrylic-film mirrors, and dielectric mirrors, were produced and tested in environmental test chambers for removing the dust layer deposited on the front surface of the mirrors. The evaluation of the prototype EDS-integrated mirrors was conducted using dust and environmental conditions that simulate the field conditions of the Mojave Desert. Test results showed thatmore » the specular reflectivity of the mirrors could be maintained at over 90% over a wide range of dust loadings ranging from 0 to 10 g/m 2, with particle diameter varying from 1 to 50 μm. The measurement of specular reflectivity (SR) was performed using a D&S Reflectometer at wavelength 660 nm. A non-contact reflectometer was designed and constructed for rapid measurement of specular reflectivity at the same wavelength. The use of this new noncontact instrument allowed us to measure SR before and after EDS activation. Several EDS prototypes were constructed and evaluated with different electrode configurations, electrode materials, and encapsulating dielectric materials.« less

In situ polarized 3He system for the Magnetism Reflectometer at the Spallation Neutron Source.

PubMed

Tong, X; Jiang, C Y; Lauter, V; Ambaye, H; Brown, D; Crow, L; Gentile, T R; Goyette, R; Lee, W T; Parizzi, A; Robertson, J L

2012-07-01

We report on the in situ polarized (3)He neutron polarization analyzer developed for the time-of-flight Magnetism Reflectometer at the Spallation Neutron Source at Oak Ridge National Laboratory. Using the spin exchange optical pumping method, we achieved a (3)He polarization of 76% ± 1% and maintained it for the entire three-day duration of the test experiment. Based on transmission measurements with unpolarized neutrons, we show that the average analyzing efficiency of the (3)He system is 98% for the neutron wavelength band of 2-5 Å. Using a highly polarized incident neutron beam produced by a supermirror bender polarizer, we obtained a flipping ratio of >100 with a transmission of 25% for polarized neutrons, averaged over the wavelength band of 2-5 Å. After the cell was depolarized for transmission measurements, it was reproducibly polarized and this performance was maintained for three weeks. A high quality polarization analysis experiment was performed on a reference sample of Fe/Cr multilayer with strong spin-flip off-specular scattering. Using a combination of the position sensitive detector, time-of-flight method, and the excellent parameters of the (3)He cell, the polarization analysis of the two-dimensional maps of reflected, refracted, and off-specular scattered intensity above and below the horizon were obtained, simultaneously.

Vitamin D Levels and Related Genetic Polymorphisms, Sun Exposure, Skin Color, and Risk of Aggressive Prostate Cancer

DTIC Science & Technology

2011-07-01

sun exposure, and dietary calcium and vitamin D intake are ascertained. Finally, the melanin content of the skin is measured using a skin reflectance...meter called a Dermaspectrometer, to measure baseline skin melanin content, which is known to inhibit vitamin D synthesis from sunlight. This...three hospitals in Chicago, along with demographic and medical information, BMI, and skin melanin content using a portable narrow-band reflectometer

Community Advisory Boards Guiding Engaged Research Efforts within a Clinical Translational Sciences Award: Key Contextual Factors Explored.

PubMed

Halladay, Jacqueline R; Donahue, Katrina E; Sleath, Betsy; Reuland, Dan; Black, Adina; Mitchell, C Madeline; Breland, Carol E; Coyne-Beasley, Tamera; Mottus, Kathleen; Watson, Sable Noelle; Lewis, Virginia; Wynn, Mysha; Corbie-Smith, Giselle

2017-01-01

Engaging stakeholders in research carries the promise of enhancing the research relevance, transparency, and speed of getting findings into practice. By describing the context and functional aspects of stakeholder groups, like those working as community advisory boards (CABs), others can learn from these experiences and operationalize their own CABs. Our objective is to describe our experiences with diverse CABs affiliated with our community engagement group within our institution's Clinical Translational Sciences Award (CTSA). We identify key contextual elements that are important to administering CABs. A group of investigators, staff, and community members engaged in a 6-month collaboration to describe their experiences of working with six research CABs. We identified the key contextual domains that illustrate how CABS are developed and sustained. Two lead authors, with experience with CABs and identifying contextual domains in other work, led a team of 13 through the process. Additionally, we devised a list of key tips to consider when devising CABs. The final domains include (1) aligned missions among stakeholders (2) resources/support, (3) defined operational processes/shared power, (4) well-described member roles, and (5) understanding and mitigating challenges. The tips are a set of actions that support the domains. Identifying key contextual domains was relatively easy, despite differences in the respective CAB's condition of focus, overall mission, or patient demographics represented. By contextualizing these five domains, other research and community partners can take an informed approach to move forward with CAB planning and engaged research.

Folding and stability of the isolated Greek key domains of the long-lived human lens proteins γD-crystallin and γS-crystallin

PubMed Central

Mills, Ishara A.; Flaugh, Shannon L.; Kosinski-Collins, Melissa S.; King, Jonathan A.

2007-01-01

The transparency of the eye lens depends on the high solubility and stability of the lens crystallin proteins. The monomeric γ-crystallins and oligomeric β-crystallins have paired homologous double Greek key domains, presumably evolved through gene duplication and fusion. Prior investigation of the refolding of human γD-crystallin revealed that the C-terminal domain folds first and nucleates the folding of the N-terminal domain. This result suggested that the human N-terminal domain might not be able to fold on its own. We constructed and expressed polypeptide chains corresponding to the isolated N- and C-terminal domains of human γD-crystallin, as well as the isolated domains of human γS-crystallin. Both circular dichroism and fluorescence spectroscopy indicated that the isolated domains purified from Escherichia coli were folded into native-like monomers. After denaturation, the isolated domains refolded efficiently at pH 7 and 37°C into native-like structures. The in vitro refolding of all four domains revealed two kinetic phases, identifying partially folded intermediates for the Greek key motifs. When subjected to thermal denaturation, the isolated N-terminal domains were less stable than the full-length proteins and less stable than the C-terminal domains, and this was confirmed in equilibrium unfolding/refolding experiments. The decrease in stability of the N-terminal domain of human γD-crystallin with respect to the complete protein indicated that the interdomain interface contributes of 4.2 kcal/mol to the overall stability of this very long-lived protein. PMID:17905830

Seismic damage identification using multi-line distributed fiber optic sensor system

NASA Astrophysics Data System (ADS)

Ou, Jinping; Hou, Shuang

2005-06-01

Determination of the actual nonlinear inelastic response mechanisms developed by civil structures such as buildings and bridges during strong earthquakes and post-earthquake damage assessment of these structures represent very difficult challenges for earthquake structural engineers. One of the main reasons is that the traditional sensor can't serve for such a long period to cover an earthquake and the seismic damage location in the structure can't be predicted in advance definitely. It is thought that the seismic damage of reinforced concrete (RC) structure can be related to the maximum response the structure, which can also be related to the cracks on the concrete. A distributed fiber optic sensor was developed to detect the cracks on the reinforced concrete structure under load. Fiber optic couples were used in the sensor system to extend the sensor system's capacity from one random point detection to more. An optical time domain reflectometer (OTDR) is employed for interrogation of the sensor signal. Fiber optic sensors are attached on the surface of the concrete by the epoxy glue. By choosing the strength of epoxy, the damage state of the concrete can be responded to the occurrence of the Fresnel scattering in the fiber optic sensor. Experiments involved monotonic loading to failure. Finally, the experimental results in terms of crack detection capability are presented and discussed.

Development of integrated damage detection system for international America's Cup class yacht structures using a fiber optic distributed sensor

NASA Astrophysics Data System (ADS)

Akiyoshi, Shimada; Naruse, Hiroshi; Uzawa, Kyoshi; Murayama, Hideaki; Kageyama, Kazuro

2000-06-01

We constructed a new health monitoring system to detect damage using a fiber optic distributed sensor, namely a Brillouin optical time domain reflectometer (BOTDR), and installed it in International America's Cup Class (IACC) yachts, the Japanese entry in America's Cup 2000. IACC yachts are designed to be as fast as possible, so it is essential that they are lightweight and encounter minimum water resistance. Advanced composite sandwich structures, made with carbon fiber reinforced plastic (CFRP) skins and a honeycomb core, are used to achieve the lightweight structure. Yacht structure designs push the strength of the materials to their limit and so it is important to detect highly stressed or damaged regions that might cause a catastrophic fracture. The BOTDR measures changes in the Brillouin frequency shift caused by distributed strain along one optical fiber. We undertook two experiments: a pulling test and a four point bending test on a composite beam. The former showed that no slippage occurred between the optical fiber glass and its coating. The latter confirmed that a debonding between the skin and the core of 300 mm length could be found with the BOTDR. Next we examined the effectiveness with which this system can assess the structural integrity of IACC yachts. The results show that our system has the potential for use as a damage detection system for smart structures.

Challenges in characterization of photonic crystal fibers

NASA Astrophysics Data System (ADS)

Borzycki, Krzysztof; Kobelke, Jens; Mergo, Pawel; Schuster, Kay

2011-05-01

We present experience with photonic crystal fiber (PCF) characterization during COST Action 299, focusing on phenomena causing errors and ways to mitigate them. PCFs developed at IPHT Jena (Germany; UMCS Lublin, Poland), designed for single mode operation were coupled to test instruments by fusion splicing to intermediate lengths of telecom single mode fibers (SMF). PCF samples were short (0.5-100 m), with 20-70 dB/km attenuation at 1310 nm and 1550 nm. Optical Time Domain Reflectometer (OTDR) was best for measuring loss as most PCFs produced strong backscattering, while variable splice losses and difficulties with PCF cleaving for optical power measurements made cutback and insertion loss measurements inaccurate. Experience with PCF handling and cleaving is also reviewed. Quality of splices to fiber under test was critical. Excitation of higher order modes produced strong "noise" during measurements of polarization parameters like PMD or PDL. Multimode propagation and vibration-induced interference precluded testing of fine dependence of PMD on temperature or strain, causing random variations comparable to true changes of PMD. OTDR measurements were not affected, but testing of short fiber sections with very different backscattering intensities puts special demands on instrument performance. Temperature testing of liquid-infiltrated PCF was time-consuming, as settling of parameters after temperature change took up to 40 minutes. PCFs were fragile, breaking below 2% linear expansion, sometimes in unusual way when twisted.

Note: 4-bounce neutron polarizer for reflectometry applications

NASA Astrophysics Data System (ADS)

Nagy, B.; Merkel, D. G.; Jakab, L.; Füzi, J.; Veres, T.; Bottyán, L.

2018-05-01

A neutron polarizer using four successive reflections on m = 2.5 supermirrors was built and installed at the GINA neutron reflectometer at the Budapest Neutron Centre. This simple setup exhibits 99.6% polarizing efficiency with 80% transmitted intensity of the selected polarization state. Due to the geometry, the higher harmonics in the incident beam are filtered out, while the optical axis of the beam remains intact for easy mounting and dismounting the device in an existing experimental setup.

Characterization and Measurements from the Infrared Grazing Angle Reflectometer

DTIC Science & Technology

2012-06-14

18 3. List of sample scatter pattern fitting values. All values were taken from Ngan’s paper ”Experimental Analysis of BRDF Models - Supplemental” [1...using a BRDF model , and the absorptance can be modeled using a Fresnel absorptance. After defining both of these values, we can calculate the power seen... BRDF model of the face of the detector. This paper will examine the case of a flat detector with some index of refraction n. This air-detector

Airborne Observation of Ocean Surface Roughness Variations Using a Combination of Microwave Radiometer and Reflectometer Systems: The Second Virginia Offshore (Virgo II) Experiment

DTIC Science & Technology

2014-03-06

from scattered satellite transmissions, was first demonstrated using Global Navigation Satellite System ( GNSS ) reflections. Recently, reflectometry has...Earth’s atmosphere. The 2012 GNSS +R workshop provided an opportunity for engineers and Earth scientists to assess the state of the art, demonstrate new...bi-static radar technique utilizes signals of opportunity transmitted from existing L-band Global Navigation Satellite Systems ( GNSS ), including GPS

Assessment of surface roughness by use of soft x-ray scattering

NASA Astrophysics Data System (ADS)

Meng, Yan-li; Wang, Yong-gang; Chen, Shu-yan; Chen, Bo

2009-08-01

A soft x-ray reflectometer with laser produced plasma source has been designed, which can work from wavelength 8nm to 30 nm and has high performance. Using the soft x-ray reflectometer above, the scattering light distribution of silicon and zerodur mirrors which have super-smooth surfaces could be measured at different incidence angle and different wavelength. The measurement when the incidence angle is 2 degree and the wavelength is 11nm has been given in this paper. A surface scattering theory of soft x-ray grazing incidence optics based on linear system theory and an inverse scattering mathematical model is introduced. The vector scattering theory of soft x-ray scattering also is stated in detail. The scattering data are analyzed by both the methods above respectively to give information about the surface profiles. On the other hand, both the two samples are measured by WYKO surface profiler, and the surface roughness of the silicon and zerodur mirror is 1.3 nm and 1.5nm respectively. The calculated results are in quantitative agreement with those measured by WYKO surface profiler, which indicates that soft x-ray scattering is a very useful tool for the evaluation of highly polished surfaces. But there still some difference among the results of different theory and WYKO, and the possible reasons of such difference have been discussed in detail.

The Southwest Research Institute ultraviolet reflectance chamber (SwURC): a far ultraviolet reflectometer

NASA Astrophysics Data System (ADS)

Winters, Gregory S.; Retherford, Kurt D.; Davis, Michael W.; Escobedo, Stephen M.; Bassett, Eric C.; Patrick, Edward L.; Nagengast, Maggie E.; Fairbanks, Matthew H.; Miles, Paul F.; Parker, Joel W.; Gladstone, G. Randall; Slater, David C.; Stern, S. Alan

2012-10-01

We designed and assembled a highly capable UV reflectometer chamber and data acquisition system to provide bidirectional scattering data of various surfaces and materials. This chamber was initially conceived to create laboratory-based UV reflectance measurements of water frost on lunar soil/regolith simulants, to support interpretation of UV reflectance data from the Lyman Alpha Mapping Project ("LAMP") instrument on-board the NASA Lunar Reconnaissance Orbiter spacecraft. A deuterium lamp illuminates surfaces and materials at a fixed 45° incident beam angle over the 115 to 200 nm range via a monochromator, while a photomultiplier tube detector is scanned to cover emission angles -85° to +85° (with a gap from -60° to -30°, due to the detector blocking the incident beam). Liquid nitrogen cools the material/sample mount when desired. The chamber can be configured to test a wide range of samples and materials using sample trays and holders. Test surfaces to date include aluminum mirrors, water ice, reflectance standards, and frozen mixtures of water and lunar soil/regolith stimulant. Future UV measurements planned include Apollo lunar samples, meteorite samples, other ices, minerals, and optical surfaces. Since this chamber may well be able to provide useful research data for groups outside Southwest Research Institute, we plan to take requests from and collaborate with others in the UV and surface reflection research community.

Production and Performance of the InFOCmicronS 20-40 keV Graded Multilayer Mirror

NASA Technical Reports Server (NTRS)

Berendse, F.; Owens, S. M.; Serlemitsos, P. J.; Tueller, J.; Chan, K.-W.; Soong, Y.; Krimm, H.; Baumgartner, W. H.; Tamura, K.; Okajima, T.;

AMOR - the time-of-flight neutron reflectometer at SINQ/PSI

NASA Astrophysics Data System (ADS)

Gupta, Mukul; Gutberlet, T.; Stahn, J.; Keller, P.; Clemens, D.

2004-07-01

The apparatus for multioptional reflectometry (AMOR) at SINQ/PSI is a versatile reflectometer operational in the time-of-flight (TOF) mode (in a wavelength range of 0.15 nm <λ < 1.3 nm) as well as in the monochromatic (theta-2theta) mode with both polarized and unpolarized neutrons. AMOR is designed to perform reflectometry measurements in horizontal sample-plane geometry which allows studying both solid-liquid and liquid-liquid interfaces. A pulsed cold neutron beam from the end position of the neutron guide is produced by a dual-chopper system (side-by-side) having two windows at 180^{circ} and rotatable with a maximum frequency of 200 Hz. In the TOF mode, the chopper frequency, width of the gating window and the chopper-detector distance can be selected independently providing a wide range of q-resolution (Delta q/q=1-10&%slash;). Remanent FeCoV/Ti : N supermirrors are used as polarizer/analyzer with a polarization efficiency of sim97&%slash;. For the monochromatic wavelength mode, a Ni/Ti multilayer is used as a monochromator, giving sim50&%slash; reflectivity at a wavelength of 0.47 nm. In the present work, a detailed description of the instrument and setting-up of the polarization option is described. Results from some of the recent studies with polarized neutrons and measurements on liquid surfaces are presented.

Upgrades to the Polarized Neutron Reflectometer Asterix at LANSCE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pynn, Roger

2015-03-16

We have upgraded the polarized neutron reflectometer, Asterix, at the Lujan Neutron Scattering Center at Los Alamos for the benefit of the research communities that study magnetic and complex-fluid films, both of which play important roles in support of the DOE’s energy mission. The upgrades to the instrument include: • A secondary spectrometer that was integrated with a Huber sample goniometer purchased with other funds just prior to the start of our project. The secondary spectrometer provides a flexible length for the scattered flight path, includes a mechanism to select among 3 alternative polarization analyzers as well as a supportmore » for new neutron detectors. Also included is an optic rail for reproducible positioning of components for Spin Echo Scattering Angle Measurement (SESAME). The entire secondary spectrometer is now non-magnetic, as required for neutron Larmor labeling. • A broad-band neutron polarizer for the incident neutron beam based on the V geometry. • A wide-angle neutron polarization analyzer • A 2d position-sensitive neutron detector • Electromagnetic coils (Wollaston prisms) for SESAME plus the associated power supplies, cooling, safety systems and integration into the data acquisition system. The upgrades allowed a nearly effortless transition between configurations required to serve the polarized neutron reflectometry community, users of the 11 T cryomagnet and users of SESAME.« less

Effects of ICRF power on SOL density profiles and LH coupling during simultaneous LH and ICRF operation on Alcator C-Mod

NASA Astrophysics Data System (ADS)

Lau, C.; Lin, Y.; Wallace, G.; Wukitch, S. J.; Hanson, G. R.; Labombard, B.; Ochoukov, R.; Shiraiwa, S.; Terry, J.

2013-09-01

A dedicated experiment during simultaneous lower hybrid (LH) and ion cyclotron range-of-frequencies (ICRF) operations is carried out to evaluate and understand the effects of ICRF power on the scrape-off-layer (SOL) density profiles and on the resultant LH coupling for a wide range of plasma parameters on Alcator C-Mod. Operation of the LH launcher with the adjacent ICRF antenna significantly degrades LH coupling while operation with the ICRF antenna that is not magnetically connected to the LH launcher minimally affects LH coupling. An X-mode reflectometer system at three poloidal locations adjacent to the LH launcher and a visible video camera imaging the LH launcher are used to measure local SOL density profile and emissivity modifications with the application of LH and LH + ICRF power. These measurements confirm that the density in front of the LH launcher depends strongly on the magnetic field line mapping of the active ICRF antenna. Reflectometer measurements also observe both ICRF-driven and LH-driven poloidal density profile asymmetries, especially a strong density depletion at certain poloidal locations in front of the LH launcher during operation with a magnetically connected ICRF antenna. The results indicate that understanding both LH-driven flows and ICRF sheath driven flows may be necessary to understand the observed density profile modifications and LH coupling results during simultaneous LH + ICRF operation.

Forensic steganalysis: determining the stego key in spatial domain steganography

NASA Astrophysics Data System (ADS)

Fridrich, Jessica; Goljan, Miroslav; Soukal, David; Holotyak, Taras

2005-03-01

This paper is an extension of our work on stego key search for JPEG images published at EI SPIE in 2004. We provide a more general theoretical description of the methodology, apply our approach to the spatial domain, and add a method that determines the stego key from multiple images. We show that in the spatial domain the stego key search can be made significantly more efficient by working with the noise component of the image obtained using a denoising filter. The technique is tested on the LSB embedding paradigm and on a special case of embedding by noise adding (the +/-1 embedding). The stego key search can be performed for a wide class of steganographic techniques even for sizes of secret message well below those detectable using known methods. The proposed strategy may prove useful to forensic analysts and law enforcement.

Analysis of a Decision Support System for CASE Tool Selection and the Specification of an Ada to SQL Abstract Interface

DTIC Science & Technology

1991-12-01

34 foreign keys" ,which are keys inherited from conlected entities, the keys would already be defined in the connected entity’s domain primiti le definition...defined for the rootnode re!ationship because all attributes are foreign keys and they are already defined in the connected entities domain primitive...can exchange data with other tools including other tools in the tool vendor’s tool 99 Upper CASE Tool Charactcrizcs set. The important attributes are

Fourier domain asymmetric cryptosystem for privacy protected multimodal biometric security

NASA Astrophysics Data System (ADS)

Choudhury, Debesh

2016-04-01

We propose a Fourier domain asymmetric cryptosystem for multimodal biometric security. One modality of biometrics (such as face) is used as the plaintext, which is encrypted by another modality of biometrics (such as fingerprint). A private key is synthesized from the encrypted biometric signature by complex spatial Fourier processing. The encrypted biometric signature is further encrypted by other biometric modalities, and the corresponding private keys are synthesized. The resulting biometric signature is privacy protected since the encryption keys are provided by the human, and hence those are private keys. Moreover, the decryption keys are synthesized using those private encryption keys. The encrypted signatures are decrypted using the synthesized private keys and inverse complex spatial Fourier processing. Computer simulations demonstrate the feasibility of the technique proposed.

Compact Instruments Measure Heat Potential

NASA Technical Reports Server (NTRS)

2009-01-01

Based in Huntsville, Alabama, AZ Technology Inc. is a woman- and veteran-owned business that offers expertise in electromechanical-optical design and advanced coatings. AZ Technology has received eight Small Business Innovation Research (SBIR) contracts with Marshall Space Flight Center for the development of spectral reflectometers and the measurement of surface thermal properties. The company uses a variety of measurement services and instruments, including the Spectrafire, a portable spectral emissometer it used to assist General Electric with the design of its award-winning Giraffe Warmer for neonatal intensive care units.

Low Performance on Mathematical Tasks in Preschoolers: The Importance of Domain-General and Domain-Specific Abilities

ERIC Educational Resources Information Center

Costa, H. M.; Nicholson, B.; Donlan, C.; Van Herwegen, J.

2018-01-01

Background: Different domain-specific and domain-general cognitive precursors play a key role in the development of mathematical abilities. The contribution of these domains to mathematical ability changes during development. Primary school-aged children who show mathematical difficulties form a heterogeneous group, but it is not clear whether…

A Review of Methods for Sensing the Nitrogen Status in Plants: Advantages, Disadvantages and Recent Advances

PubMed Central

Muñoz-Huerta, Rafael F.; Guevara-Gonzalez, Ramon G.; Contreras-Medina, Luis M.; Torres-Pacheco, Irineo; Prado-Olivarez, Juan; Ocampo-Velazquez, Rosalia V.

2013-01-01

Nitrogen (N) plays a key role in the plant life cycle. It is the main plant mineral nutrient needed for chlorophyll production and other plant cell components (proteins, nucleic acids, amino acids). Crop yield is affected by plant N status. Thus, the optimization of nitrogen fertilization has become the object of intense research due to its environmental and economic impact. This article focuses on reviewing current methods and techniques used to determine plant N status. Kjeldahl digestion and Dumas combustion have been used as reference methods for N determination in plants, but they are destructive and time consuming. By using spectroradiometers, reflectometers, imagery from satellite sensors and digital cameras, optical properties have been measured to estimate N in plants, such as crop canopy reflectance, leaf transmittance, chlorophyll and polyphenol fluorescence. High correlation has been found between optical parameters and plant N status, and those techniques are not destructive. However, some drawbacks include chlorophyll saturation, atmospheric and soil interference, and the high cost of instruments. Electrical properties of plant tissue have been used to estimate quality in fruits, and water content in plants, as well as nutrient deficiency, which suggests that they have potential for use in plant N determination. PMID:23959242

Phosphate homeostasis in the yeast Saccharomyces cerevisiae, the key role of the SPX domain-containing proteins.

PubMed

Secco, David; Wang, Chuang; Shou, Huixia; Whelan, James

2012-02-17

In the yeast Saccharomyces cerevisiae, a working model for nutrient homeostasis in eukaryotes, inorganic phosphate (Pi) homeostasis is regulated by the PHO pathway, a set of phosphate starvation induced genes, acting to optimize Pi uptake and utilization. Among these, a subset of proteins containing the SPX domain has been shown to be key regulators of Pi homeostasis. In this review, we summarize the recent progresses in elucidating the mechanisms controlling Pi homeostasis in yeast, focusing on the key roles of the SPX domain-containing proteins in these processes, as well as describing the future challenges and opportunities in this fast-moving field. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

High speed reflectometer for EUV mask-blanks

NASA Astrophysics Data System (ADS)

Wies, Christian; Lebert, Rainer; Jagle, Bernhard; Juschkin, L.; Sobel, F.; Seitz, H.; Walter, Ronny; Laubis, C.; Scholze, F.; Biel, W.; Steffens, O.

2005-06-01

AIXUV GmbH and partners have developed a high speed Reflectometer for EUV mask-blanks which is fully compliant with the SEMI-standard P38 for EUV-mask-blank metrology. The system has been installed in June 2004 at SCHOTT Lithotec AG. It features high throughput, high lateral and spectral resolution, high reproducibility and low absolute uncertainty. Using AIXUV's EUV-LAMP and debris mitigation, low cost-of-ownership and high availability is expected. The spectral reflectance of up to 3 mask-blanks per hour can be measured with at least 20 spots each. The system is push button-controlled. Results are stored in CSV file format. For a spot size of 0.1x1 mm2, 2000 spectral channels of 1.6 pm bandwidth are recorded from 11.6 nm to 14.8 nm. The reflectance measurement is based on the comparison of the sample under test to two reference mirrors calibrated at the PTB radiometry laboratory at BESSY II. The three reflection spectra are recorded simultaneously. For each spot more than 107 photons are accumulated in about 20 s, providing statistical reproducibility below 0.2% RMS. The total uncertainty is below 0.5% absolute. Wavelength calibration better than 1 pm RMS over the whole spectral range is achieved by reference to NIST published wavelengths of about 100 xenon emission lines. It is consistent with the wavelength of the krypton 3d-5p absorption resonance at 13.5947 nm to better than 2 pm.

High speed reflectometer for EUV mask-blanks

NASA Astrophysics Data System (ADS)

Wies, C.; Lebert, R.; Jaegle, B.; Juschkin, L.; Sobel, F.; Seitz, H.; Walter, R.; Laubis, C.; Scholze, F.; Biel, W.; Steffens, O.

2005-05-01

AIXUV GmbH and partners have developed a high speed Reflectometer for EUV mask-blanks which is fully compliant with the SEMI-standard P38 for EUV-mask-blank metrology. The system has been installed in June 2004 at SCHOTT Lithotec AG. It features high throughput, high lateral and spectral resolution, high reproduci-bility and low absolute uncertainty. Using AIXUV's EUV-LAMP and debris mitigation, low cost-of-ownership and high availability is expected. The spectral reflectance of up to 3 mask-blanks per hour can be measured with at least 20 spots each. The system is push button-controlled. Results are stored in CSV file format. For a spot size of 0.1×1 mm2, 2000 spectral chan-nels of 1.6 pm bandwidth are recorded from 11.6 nm to 14.8 nm. The reflectance measurement is based on the comparison of the sample under test to two reference mirrors calibrated at the PTB radiometry laboratory at BESSY II. The three reflection spectra are recorded simultaneously. For each spot more than 107 photons are ac-cumulated in about 20 s, providing statistical reproducibility below 0.2 % RMS. The total uncertainty is below 0.5 % absolute. Wavelength calibration better than 1 pm RMS over the whole spectral range is achieved by refe-rence to NIST published wavelengths of about 100 xenon emission lines. It is consistent with the wavelength of the krypton 3d-5p absorption resonance at 13.5947 nm to better than 2 pm.

Leading School-Wide Improvement in Low-Performing Schools Facing Conditions of Accountability: Key Actions and Considerations

ERIC Educational Resources Information Center

Cosner, Shelby; Jones, Mary F.

2016-01-01

Purpose: The purpose of this paper is to advance a framework that identifies three key domains of work and a set of more nuanced considerations and actions within each domain for school leaders seeking to improve school-wide student learning in low-performing schools facing conditions of accountability. Design/methodology/approach: Review of…

Tunable fiber Bragg grating ring lasers using macro fiber composite actuators

NASA Astrophysics Data System (ADS)

Geddis, Demetris L.; Allison, Sidney G.; Shams, Qamar A.

2006-10-01

The research reported herein includes the fabrication of a tunable optical fiber Bragg grating (FBG) fiber ring laser (FRL)1 from commercially available components as a high-speed alternative tunable laser source for NASA Langley's optical frequency domain reflectometer (OFDR) interrogator, which reads low reflectivity FBG sensors. A Macro-Fiber Composite (MFC) actuator invented at NASA Langley Research Center (LaRC) was selected to tune the laser. MFC actuators use a piezoelectric sheet cut into uniaxially aligned rectangular piezo-fibers surrounded by a polymer matrix and incorporate interdigitated electrodes to deliver electric fields along the length of the piezo-fibers. This configuration enables MFC actuators to produce displacements larger than the original uncut piezoelectric sheet. The FBG filter was sandwiched between two MFC actuators, and when strained, produced approximately 3.62 nm of wavelength shift in the FRL when biasing the MFC actuators from -500 V to 2000 V. This tunability range is comparable to that of other tunable lasers and is adequate for interrogating FBG sensors using OFDR technology. Three different FRL configurations were studied. Configuration A examined the importance of erbium-doped fiber length and output coupling. Configuration B demonstrated the importance of the FBG filter. Configuration C added an output coupler to increase the output power and to isolate the filter. Only configuration C was tuned because it offered the best optical power output of the three configurations. Use of Plastic Optical Fiber (POF) FBG's holds promise for enhanced tunability in future research.

Tunable Fiber Bragg Grating Ring Lasers using Macro Fiber Composite Actuators

NASA Technical Reports Server (NTRS)

Geddis, Demetris L.; Allison, Sidney G.; Shams, Qamar A.

2006-01-01

The research reported herein includes the fabrication of a tunable optical fiber Bragg grating (FBG) fiber ring laser (FRL)1 from commercially available components as a high-speed alternative tunable laser source for NASA Langley s optical frequency domain reflectometer (OFDR) interrogator, which reads low reflectivity FBG sensors. A Macro-Fiber Composite (MFC) actuator invented at NASA Langley Research Center (LaRC) was selected to tune the laser. MFC actuators use a piezoelectric sheet cut into uniaxially aligned rectangular piezo-fibers surrounded by a polymer matrix and incorporate interdigitated electrodes to deliver electric fields along the length of the piezo-fibers. This configuration enables MFC actuators to produce displacements larger than the original uncut piezoelectric sheet. The FBG filter was sandwiched between two MFC actuators, and when strained, produced approximately 3.62 nm of wavelength shift in the FRL when biasing the MFC actuators from 500 V to 2000 V. This tunability range is comparable to that of other tunable lasers and is adequate for interrogating FBG sensors using OFDR technology. Three different FRL configurations were studied. Configuration A examined the importance of erbium-doped fiber length and output coupling. Configuration B demonstrated the importance of the FBG filter. Configuration C added an output coupler to increase the output power and to isolate the filter. Only configuration C was tuned because it offered the best optical power output of the three configurations. Use of Plastic Optical Fiber (POF) FBG s holds promise for enhanced tunability in future research.

Feasibility study for distributed dose monitoring in ionizing radiation environments with standard and custom-made optical fibers

NASA Astrophysics Data System (ADS)

Van Uffelen, Marco; Berghmans, Francis; Brichard, Benoit; Borgermans, Paul; Decréton, Marc C.

2002-09-01

Optical fibers stimulate much interest since many years for their potential use in various nuclear environments, both for radiation tolerant and EMI-free data communication as well as for distributed sensing. Besides monitoring temperature and stress, measuring ionizing doses with optical fibers is particularly essential in applications such as long-term nuclear waste disposal monitoring, and for real-time aging monitoring of power and signal cables installed inside a reactor containment building. Two distinct options exist to perform optical fiber dosimetry. First, find an accurate model for a restricted application field that accounts for all the parameters that influence the radiation response of a standard fiber, or second, develop a dedicated fiber with a response that will solely depend on the deposited energy. Using various models presented in literature, we evaluate both standard commercially available and custom-made optical fibers under gamma radiation, particularly for distributed dosimetry applications with an optical time domain reflectometer (OTDR). We therefore present the radiation induced attenuation at near-infrared telecom wavelengths up to MGy total dose levels, with dose rates ranging from about 1 Gy/h up to 1 kGy/h, whereas temperature was raised step-wise from 25 °C to 85 °C. Our results allow to determine and compare the practical limitations of distributed dose measurements with both fiber types in terms of temperature sensitivity, dose estimation accuracy and spatial resolution.

Use of soil moisture probes to estimate ground water recharge at an oil spill site

USGS Publications Warehouse

Delin, G.N.; Herkelrath, W.N.

2005-01-01

Soil moisture data collected using an automated data logging system were used to estimate ground water recharge at a crude oil spill research site near Bemidji, Minnesota. Three different soil moisture probes were tested in the laboratory as well as the field conditions of limited power supply and extreme weather typical of northern Minnesota: a self-contained reflectometer probe, and two time domain reflectometry (TDR) probes, 30 and 50 cm long. Recharge was estimated using an unsaturated zone water balance method. Recharge estimates for 1999 using the laboratory calibrations were 13 to 30 percent greater than estimates based on the factory calibrations. Recharge indicated by the self-contained probes was 170 percent to 210 percent greater than the estimates for the TDR probes regardless of calibration method. Results indicate that the anomalously large recharge estimates for the self-contained probes are not the result of inaccurate measurements of volumetric moisture content, but result from the presence of crude oil, or bore-hole leakage. Of the probes tested, the 50 cm long TDR probe yielded recharge estimates that compared most favorably to estimates based on a method utilizing water table fluctuations. Recharge rates for this probe represented 24 to 27 percent of 1999 precipitation. Recharge based on the 30 cm long horizontal TDR probes was 29 to 37 percent of 1999 precipitation. By comparison, recharge based on the water table fluctuation method represented about 29 percent of precipitation. (JAWRA) (Copyright ?? 2005).

Real-time investigation of protein unfolding at an air–water interface at the 1 s time scale

PubMed Central

Yano, Yohko F.; Arakawa, Etsuo; Voegeli, Wolfgang; Matsushita, Tadashi

2013-01-01

Protein unfolding at an air–water interface has been demonstrated such that the X-ray reflectivity can be measured with an acquisition time of 1 s using a recently developed simultaneous multiple-angle–wavelength-dispersive X-ray reflectometer. This has enabled the electron density profile of the adsorbed protein molecules to be obtained in real time. A globular protein, lysozyme, adsorbed at the air–water interface is found to unfold into a flat shape within 1 s. PMID:24121352

High-resolution reflectometer for monitoring of biological samples

NASA Astrophysics Data System (ADS)

Men, Liqiu; Lu, Ping; Chen, Qiying

2008-06-01

High-resolution optical low-coherence reflectometry is applied to monitor biological samples. It has been found that the reflectivity of aged cow's milk is significantly lower than that of the fresh milk with a difference of 5.35dB. During the process of heating the fresh milk at a constant temperature of 80°C, the reflectivity of the milk gradually decreases with the increase of the heating duration. The technique is proved to be effective in monitoring the change in the refractive index of the sample.

First tests of a MIEZE (modulated intensity by Zero effort)-type instrument on a pulsed neutron source

NASA Astrophysics Data System (ADS)

Bleuel, M.; Bröll, M.; Lang, E.; Littrell, K.; Gähler, R.; Lal, J.

2006-01-01

In this paper we report the results of our first tests of a novel proof-of-principle instrument developed at the IPNS, Argonne. The experiment was performed on the time of flight POSY1 instrument, the polarized reflectometer at the IPNS, which was modified to accommodate the apparatus. Two sets of RF-flippers were tested together, generating a modulated intensity by zero effort (MIEZE)-type neutron resonant spin echo signal which was observed at the detector using a wide neutron wavelength band.

Managed Behavioral Health Care: An Instrument to Characterize Critical Elements of Public Sector Programs

PubMed Central

Ridgely, M Susan; Giard, Julienne; Shern, David; Mulkern, Virginia; Burnam, M Audrey

2002-01-01

Objective To develop an instrument to characterize public sector managed behavioral health care arrangements to capture key differences between managed and “unmanaged” care and among managed care arrangements. Study Design The instrument was developed by a multi-institutional group of collaborators with participation of an expert panel. Included are six domains predicted to have an impact on access, service utilization, costs, and quality. The domains are: characteristics of the managed care plan, enrolled population, benefit design, payment and risk arrangements, composition of provider networks, and accountability. Data are collected at three levels: managed care organization, subcontractor, and network of service providers. Data Collection Methods Data are collected through contract abstraction and key informant interviews. A multilevel coding scheme is used to organize the data into a matrix along key domains, which is then reviewed and verified by the key informants. Principal Findings This instrument can usefully differentiate between and among Medicaid fee-for-service programs and Medicaid managed care plans along key domains of interest. Beyond documenting basic features of the plans and providing contextual information, these data will support the refinement and testing of hypotheses about the impact of public sector managed care on access, quality, costs, and outcomes of care. Conclusions If managed behavioral health care research is to advance beyond simple case study comparisons, a well-conceptualized set of instruments is necessary. PMID:12236386

Overview of Megaprogramming Course: Lectures and Exercises. Version 02. 00.03

DTIC Science & Technology

1994-02-01

schedule to be presented (e.g., so it looks like a calendar or just a list for each day followed by the time) It might be useftl to have a separate text ...machines, yet enough differences, that it makes sense to study their similarities and differences. "* What would the domain engineer do in this domain...of the item, followed by the ENTER key. If you need help, press the F1 key. You can use the backspace key to remove the last character you typed. When

Report of the key-comparison of spectral diffuse reflectance (EURAMET.PR-K5) (Ref. 619)

NASA Astrophysics Data System (ADS)

Andor, György; Gál, Péter

2018-01-01

This report details the final results of the EURAMET comparison on regular spectral transmittance carried out between 2006 and 2016. The aim of this comparison was to check the agreement of measurement of the spectral diffuse reflectance among participants, using the measurement geometry of d/0 or 0/d in the wavelength range of 360 nm to 780 nm at 20 nm increment. We used a star type comparison: first the participants sent their samples to the pilot, than the pilot measured all the samples of the participants and sent them back. The participants measured the samples and sent them to the pilot for control measurement. Six standards were used as reference standards in order to maintain the scale during the comparison. These were three samples of BCR-406 opal glasses (BCR 30506; BCR 30303; BCR 30704), an MC20 Russian opal glass (MC 4777) and two samples made of pressed halon (polytetrafluoroethylene) powder (halon 2007A; halon 2007C). These six samples were designated as the Comparison reference standards. The diffuse reflectance was initially measured on the OMH (BFKH) absolute reflectometer. The link to the CCPR-K5 results was BFKH, and the check on BFKH was the PTB results who also participated in the CCPR-K5 comparison. The participants were GUM, INM, LNE, METAS, BFKH, PTB, SP. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCPR, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

Current at domain walls, roughly speaking: nanoscales studies of disorder roughening and conduction

NASA Astrophysics Data System (ADS)

Paruch, Patrycja

2013-03-01

Domain walls in (multi)ferroic materials are the thin elastic interfaces separating regions with different orientations of magnetisation, electric polarisation, or spontaneous strain. Understanding their behaviour, and controlling domain size and stability, is key for their integration into applications, while fundamentally, domain walls provide an excellent model system in which the rich physics of disordered elastic interfaces can be accesses. In addition, domain walls can present novel properties, quite different from those of their parent materials, making them potentially useful as active components in future nano-devices. Here, we present our atomic force microscopy studies of ferroelectric domain walls in epitaxial Pb(Zr0.2Ti0.8)O3 and BiFeO3 thin films, in which we use piezorespose force microscopy to show unusual domain wall roughening behaviour, with very localised disorder regions in the sample leading to a complex, multi-affine scaling of the domain wall shape. We also show the effects of temperature, environmental conditions, and defects on switching dynamics and domain wall roughness. We combine these observations with parallel conductive-tip atomic force microscopy current measurements, which also show highly localised variations in conduction, and highlight the key role played by oxygen vacancies in the observed domain wall conduction.

Key factors influencing allied health research capacity in a large Australian metropolitan health district

PubMed Central

Alison, Jennifer A; Zafiropoulos, Bill; Heard, Robert

2017-01-01

Objective The aim of this study was to identify key factors affecting research capacity and engagement of allied health professionals working in a large metropolitan health service. Identifying such factors will assist in determining strategies for building research capacity in allied health. Materials and methods A total of 276 allied health professionals working within the Sydney Local Health District (SLHD) completed the Research Capacity in Context Tool (RCCT) that measures research capacity and culture across three domains: organization, team, and individual. An exploratory factor analysis was undertaken to identify common themes within each of these domains. Correlations were performed between demographic variables and the identified factors to determine possible relationships. Results Research capacity and culture success/skill levels were reported to be higher within the organization and team domains compared to the individual domain (median [interquartile range, IQR] 6 [5–8], 6 [5–8], 5 [3–7], respectively; Friedman χ2(2)=42.04, p<0.001). Exploratory factor analyses were performed to identify factors that were perceived by allied health respondents to affect research capacity. Factors identified within the organization domain were infrastructure for research (eg, funds and equipment) and research culture (eg, senior manager’s support for research); within the team domain the factors were research orientation (eg, dissemination of results at research seminars) and research support (eg, providing staff research training). Within the individual domain, only one factor was identified which was the research skill of the individual (eg, literature evaluation, submitting ethics applications and data analysis, and writing for publication). Conclusion The reported skill/success levels in research were lower for the individual domain compared to the organization or team domains. Key factors were identified in each domain that impacted on allied health research capacity. As these factors were different in each domain, various strategies may be required at the level of the organization, team, and individual to support and build allied health research capacity. PMID:28860795

Evaluation of low-frequency operational limit of proposed ITER low-field-side reflectometer waveguide run including miter bends.

PubMed

Wang, G; Peebles, W A; Doyle, E J; Crocker, N A; Wannberg, C; Lau, C; Hanson, G R; Doane, J L

2017-10-01

The present design concept for the ITER low-field-side reflectometer transmission line (TL) consists of an ∼40 m long, 6.35 cm diameter helically corrugated waveguide (WG) together with ten 90° miter bends. This paper presents an evaluation of the TL performance at low frequencies (33-50 GHz) where the predicted HE 11 mode ohmic and mode conversion losses start to increase significantly. Quasi-optical techniques were used to form a near Gaussian beam to efficiently couple radiation in this frequency range into the WG. It was observed that the output beams from the guide remained linearly polarized with cross-polarization power levels of ∼1.5%-3%. The polarization rotation due to the helical corrugations was in the range ∼1°-3°. The radiated beam power profiles typically show excellent Gaussian propagation characteristics at distances >20 cm from the final exit aperture. The round trip propagation loss was found to be ∼2.5 dB at 50 GHz and ∼6.5 dB at 35 GHz, showing an inverse increase with frequency. This was consistent with updated calculations of miter bend and ohmic losses. At low frequencies (33-50 GHz), the mode purity remained very good at the exit of the waveguide, and the losses are perfectly acceptable for operation in ITER. The primary challenge may come from the future addition of a Gaussian telescope and other filter components within the corrugated guide, which will likely introduce additional perturbations to the beam profile and an increase in mode-conversion loss.

Bubble velocity, diameter, and void fraction measurements in a multiphase flow using fiber optic reflectometer

NASA Astrophysics Data System (ADS)

Lim, Ho-Joon; Chang, Kuang-An; Su, Chin B.; Chen, Chi-Yueh

2008-12-01

A fiber optic reflectometer (FOR) technique featuring a single fiber probe is investigated for its feasibility of measuring the bubble velocity, diameter, and void fraction in a multiphase flow. The method is based on the interference of the scattered signal from the bubble surface with the Fresnel reflection signal from the tip of the optical fiber. Void fraction is obtained with a high accuracy if an appropriate correction is applied to compensate the underestimated measurement value. Velocity information is accurately obtained from the reflected signals before the fiber tip touches the bubble surface so that several factors affecting the traditional dual-tip probes such as blinding, crawling, and drifting effects due to the interaction between the probe and bubbles can be prevented. The coherent signals reflected from both the front and rear ends of a bubble can provide velocity information. Deceleration of rising bubbles and particles due to the presence of the fiber probe is observed when they are very close to the fiber tip. With the residence time obtained, the bubble chord length can be determined by analyzing the coherent signal for velocity determination before the deceleration starts. The bubble diameters are directly obtained from analyzing the signals of the bubbles that contain velocity information. The chord lengths of these bubbles measured by FOR represent the bubble diameters when the bubble shape is spherical or represent the minor axes when the bubble shape is ellipsoidal. The velocity and size of bubbles obtained from the FOR measurements are compared with those obtained simultaneously using a high speed camera.

Density perturbation mode structure of high frequency compressional and global Alfvén eigenmodes in the National Spherical Torus Experiment using a novel reflectometer analysis technique

NASA Astrophysics Data System (ADS)

Crocker, N. A.; Kubota, S.; Peebles, W. A.; Rhodes, T. L.; Fredrickson, E. D.; Belova, E.; Diallo, A.; LeBlanc, B. P.; Sabbagh, S. A.

2018-01-01

Reflectometry measurements of compressional (CAE) and global (GAE) Alfvén eigenmodes are analyzed to obtain the amplitude and spatial structure of the density perturbations associated with the modes. A novel analysis technique developed for this purpose is presented. The analysis also naturally yields the amplitude and spatial structure of the density contour radial displacement, which is found to be 2-4 times larger than the value estimated directly from the reflectometer measurements using the much simpler ‘mirror approximation’. The modes were driven by beam ions in a high power (6 MW) neutral beam heated H-mode discharge (#141398) in the National Spherical Torus Experiment. The results of the analysis are used to assess the contribution of the modes to core energy transport and ion heating. The total displacement amplitude of the modes, which is shown to be larger than previously estimated (Crocker et al 2013 Nucl. Fusion 53 43017), is compared to the predicted threshold (Gorelenkov et al 2010 Nucl. Fusion 50 84012) for the anomalously high heat diffusion inferred from transport modeling in similar NSTX discharges. The results of the analysis also have strong implications for the energy transport via coupling of CAEs to kinetic Alfvén waves seen in simulations with the Hybrid MHD code (Belova et al 2015 Phys. Rev. Lett. 115 15001). Finally, the amplitudes of the observed CAEs fall well below the threshold for causing significant ion heating by stochastic velocity space diffusion (Gates et al 2001 Phys. Rev. Lett. 87 205003).

Evaluation of low-frequency operational limit of proposed ITER low-field-side reflectometer waveguide run including miter bends

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Guiding; Peebles, W. A.; Doyle, E. J.

The present design concept for the ITER low-field-side reflectometer transmission line (TL) consists of an ~40 m long, 6.35 cm diameter helically corrugated waveguide (WG) together with ten 90° miter bends. This paper presents an evaluation of the TL performance at low frequencies (33-50 GHz) where the predicted HE11 mode ohmic and mode conversion losses start to increase significantly. Quasi-optical techniques were used to form a near Gaussian beam to efficiently couple radiation in this frequency range into the WG. We observed that the output beams from the guide remained linearly polarized with cross-polarization power levels of ~1.5%-3%. The polarizationmore » rotation due to the helical corrugations was in the range ~1°-3°. The radiated beam power profiles typically show excellent Gaussian propagation characteristics at distances >20 cm from the final exit aperture. The round trip propagation loss was found to be ~2.5 dB at 50 GHz and ~6.5 dB at 35 GHz, showing an inverse increase with frequency. This was consistent with updated calculations of miter bend and ohmic losses. At low frequencies (33-50 GHz), the mode purity remained very good at the exit of the waveguide, and the losses are perfectly acceptable for operation in ITER. Finally, the primary challenge may come from the future addition of a Gaussian telescope and other filter components within the corrugated guide, which will likely introduce additional perturbations to the beam profile and an increase in mode-conversion loss.« less

Solution Binding and Structural Analyses Reveal Potential Multidrug Resistance Functions for SAV2435 and CTR107 and Other GyrI-like Proteins.

PubMed

Moreno, Andrew; Froehlig, John R; Bachas, Sharrol; Gunio, Drew; Alexander, Teressa; Vanya, Aaron; Wade, Herschel

2016-08-30

Multidrug resistance (MDR) refers to the acquired ability of cells to tolerate a broad range of toxic compounds. One mechanism cells employ is to increase the level of expression of efflux pumps for the expulsion of xenobiotics. A key feature uniting efflux-related mechanisms is multidrug (MD) recognition, either by efflux pumps themselves or by their transcriptional regulators. However, models describing MD binding by MDR effectors are incomplete, underscoring the importance of studies focused on the recognition elements and key motifs that dictate polyspecific binding. One such motif is the GyrI-like domain, which is found in several MDR proteins and is postulated to have been adapted for small-molecule binding and signaling. Here we report the solution binding properties and crystal structures of two proteins containing GyrI-like domains, SAV2435 and CTR107, bound to various ligands. Furthermore, we provide a comparison with deposited crystal structures of GyrI-like proteins, revealing key features of GyrI-like domains that not only support polyspecific binding but also are conserved among GyrI-like domains. Together, our studies suggest that GyrI-like domains perform evolutionarily conserved functions connected to multidrug binding and highlight the utility of these types of studies for elucidating mechanisms of MDR.

Optical image encryption using QR code and multilevel fingerprints in gyrator transform domains

NASA Astrophysics Data System (ADS)

Wei, Yang; Yan, Aimin; Dong, Jiabin; Hu, Zhijuan; Zhang, Jingtao

2017-11-01

A new concept of GT encryption scheme is proposed in this paper. We present a novel optical image encryption method by using quick response (QR) code and multilevel fingerprint keys in gyrator transform (GT) domains. In this method, an original image is firstly transformed into a QR code, which is placed in the input plane of cascaded GTs. Subsequently, the QR code is encrypted into the cipher-text by using multilevel fingerprint keys. The original image can be obtained easily by reading the high-quality retrieved QR code with hand-held devices. The main parameters used as private keys are GTs' rotation angles and multilevel fingerprints. Biometrics and cryptography are integrated with each other to improve data security. Numerical simulations are performed to demonstrate the validity and feasibility of the proposed encryption scheme. In the future, the method of applying QR codes and fingerprints in GT domains possesses much potential for information security.

Diffraction gratings metrology and ray-tracing results for an XUV Raman spectrometer at FLASH

PubMed Central

Dziarzhytski, Siarhei; Siewert, Frank; Gwalt, Grzegorz; Seliger, Tino; Rübhausen, Michael; Weigelt, Holger; Brenner, Günter

2018-01-01

The extreme-ultraviolet double-stage imaging Raman spectrometer is a permanent experimental endstation at the plane-grating monochromator beamline branch PG1 at FLASH at DESY in Hamburg, Germany. This unique instrument covers the photon energy range from 20 to 200 eV with high energy resolution of about 2 to 20 meV (design values) featuring an efficient elastic line suppression as well as effective stray light rejection. Such a design enables studies of low-energy excitations like, for example, phonons in solids close to the vicinity of the elastic line. The Raman spectrometer effectively operates with four reflective off-axial parabolic mirrors and two plane-grating units. The optics quality and their precise alignment are crucial to guarantee best performance of the instrument. Here, results on a comprehensive investigation of the quality of the spectrometer diffraction gratings are presented. The gratings have been characterized by ex situ metrology at the BESSY-II Optics Laboratory, employing slope measuring deflectometry and interferometry as well as atomic force microscopy studies. The efficiency of these key optical elements has been measured at the at-wavelength metrology laboratory using the reflectometer at the BESSY-II Optics beamline. Also, the metrology results are discussed with respect to the expected resolving power of the instrument by including them in ray-tracing studies of the instrument. PMID:29271763

A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

PubMed Central

Qin, Feng

2015-01-01

The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

Exploiting domain information for Word Sense Disambiguation of medical documents.

PubMed

Stevenson, Mark; Agirre, Eneko; Soroa, Aitor

2012-01-01

Current techniques for knowledge-based Word Sense Disambiguation (WSD) of ambiguous biomedical terms rely on relations in the Unified Medical Language System Metathesaurus but do not take into account the domain of the target documents. The authors' goal is to improve these methods by using information about the topic of the document in which the ambiguous term appears. The authors proposed and implemented several methods to extract lists of key terms associated with Medical Subject Heading terms. These key terms are used to represent the document topic in a knowledge-based WSD system. They are applied both alone and in combination with local context. A standard measure of accuracy was calculated over the set of target words in the widely used National Library of Medicine WSD dataset. The authors report a significant improvement when combining those key terms with local context, showing that domain information improves the results of a WSD system based on the Unified Medical Language System Metathesaurus alone. The best results were obtained using key terms obtained by relevance feedback and weighted by inverse document frequency.

Exploiting domain information for Word Sense Disambiguation of medical documents

PubMed Central

Agirre, Eneko; Soroa, Aitor

2011-01-01

Objective Current techniques for knowledge-based Word Sense Disambiguation (WSD) of ambiguous biomedical terms rely on relations in the Unified Medical Language System Metathesaurus but do not take into account the domain of the target documents. The authors' goal is to improve these methods by using information about the topic of the document in which the ambiguous term appears. Design The authors proposed and implemented several methods to extract lists of key terms associated with Medical Subject Heading terms. These key terms are used to represent the document topic in a knowledge-based WSD system. They are applied both alone and in combination with local context. Measurements A standard measure of accuracy was calculated over the set of target words in the widely used National Library of Medicine WSD dataset. Results and discussion The authors report a significant improvement when combining those key terms with local context, showing that domain information improves the results of a WSD system based on the Unified Medical Language System Metathesaurus alone. The best results were obtained using key terms obtained by relevance feedback and weighted by inverse document frequency. PMID:21900701

Far-infrared BRDFs and reflectance spectra of candidate SOFIA telescope, cavity, and focal-plane instrument surfaces

NASA Astrophysics Data System (ADS)

Meyer, Allan W.; Smith, Sheldon M.; Koerber, Christopher T.

2000-06-01

The far-infrared reflectance and scattering properties of telescope surfaces, surrounding cavity walls, and surfaces within focal-plane instruments can be significant contributors to background noise. Radiation from sources well off-axis, such as the earth, moon or aircraft engines may be multiply scattered by the cavity walls and/or surface facets of a complex telescope structure. The Non-Specular Reflectometer at NASA Ames Research Center was reactivated and upgraded, and used to measure reflectance and Bi- directional Reflectance Distribution Functions for samples of planned telescope system structural materials and associated surface treatments.

Return to the red planet

NASA Astrophysics Data System (ADS)

Nichols, Robert G.

1992-10-01

The paper discusses the type of data which will be collected by the NASA's Mars Observer spacecraft when it reaches the planet next year. These will include measurements on the Martian magnetic field, the volcanic activity, the dust storms, seasonal weather cycles, and the planet's atmosphere and gravitational field. The Mars Observer's instruments include a magnetometer, an electron reflectometer, an IR radiometer, a laser altimeter, a thermal-emission spectrometer, a gamma-ray spectrometer, a camera, and a radio system. The program is counting on the vehicle's longevity so that it can participate in a Russian mission due to arrive at Mars in September 1995.

Study of Optical Fiber Sensors for Cryogenic Temperature Measurements.

PubMed

De Miguel-Soto, Veronica; Leandro, Daniel; Lopez-Aldaba, Aitor; Beato-López, Juan Jesus; Pérez-Landazábal, José Ignacio; Auguste, Jean-Louis; Jamier, Raphael; Roy, Philippe; Lopez-Amo, Manuel

2017-11-30

In this work, the performance of five different fiber optic sensors at cryogenic temperatures has been analyzed. A photonic crystal fiber Fabry-Pérot interferometer, two Sagnac interferometers, a commercial fiber Bragg grating (FBG), and a π-phase shifted fiber Bragg grating interrogated in a random distributed feedback fiber laser have been studied. Their sensitivities and resolutions as sensors for cryogenic temperatures have been compared regarding their advantages and disadvantages. Additionally, the results have been compared with the given by a commercial optical backscatter reflectometer that allowed for distributed temperature measurements of a single mode fiber.

Study of Optical Fiber Sensors for Cryogenic Temperature Measurements

PubMed Central

Leandro, Daniel; Lopez-Aldaba, Aitor; Beato-López, Juan Jesus; Pérez-Landazábal, José Ignacio; Auguste, Jean-Louis; Jamier, Raphael; Roy, Philippe; Lopez-Amo, Manuel

2017-01-01

In this work, the performance of five different fiber optic sensors at cryogenic temperatures has been analyzed. A photonic crystal fiber Fabry-Pérot interferometer, two Sagnac interferometers, a commercial fiber Bragg grating (FBG), and a π-phase shifted fiber Bragg grating interrogated in a random distributed feedback fiber laser have been studied. Their sensitivities and resolutions as sensors for cryogenic temperatures have been compared regarding their advantages and disadvantages. Additionally, the results have been compared with the given by a commercial optical backscatter reflectometer that allowed for distributed temperature measurements of a single mode fiber. PMID:29189755

Exploring the limits of sequence and structure in a variant βγ-crystallin domain of the protein absent in melanoma-1 (AIM1)

PubMed Central

Aravind, Penmatsa; Wistow, Graeme; Sharma, Yogendra; Sankaranarayanan, Rajan

2008-01-01

βγ-Crystallins belong to a superfamily of proteins in prokaryotes and eukaryotes that are based on duplications of a characteristic, highly conserved Greek Key motif. Most members of the superfamily in vertebrates are structural proteins of the eye lens that contain four motifs arranged as two structural domains. Absent in melanoma-1 (AIM1), an unusual member of the superfamily whose expression is associated with suppression of malignancy in melanoma, contains 12 βγ-crystallin motifs in six domains. Some of these motifs diverge considerably from the canonical motif sequence. AIM1g1, the first βγ-crystallin domain of AIM1, is the most variant of βγ-crystallin domains currently known. In order to understand the limits of sequence variation on the structure, we report the crystal structure of AIM1g1 at 1.9Å resolution. In spite of having changes in key residues, the domain retains the overall βγ-crystallin fold. The domain also contains an unusual extended surface loop that significantly alters the shape of the domain and its charge profile. This structure illustrates the resilience of the βγ fold to considerable sequence changes and its remarkable ability to adapt for novel functions. PMID:18582473

UXDs-Driven Transferring Method from TRIZ Solution to Domain Solution

NASA Astrophysics Data System (ADS)

Ma, Lihui; Cao, Guozhong; Chang, Yunxia; Wei, Zihui; Ma, Kai

The translation process from TRIZ solutions to domain solutions is an analogy-based process. TRIZ solutions, such as 40 inventive principles and the related cases, are medium-solutions for domain problems. Unexpected discoveries (UXDs) are the key factors to trigger designers to generate new ideas for domain solutions. The Algorithm of UXD resolving based on Means-Ends Analysis(MEA) is studied and an UXDs-driven transferring method from TRIZ solution to domain solution is formed. A case study shows the application of the process.

Structural Landscape of the Proline-Rich Domain of Sos1 Nucleotide Exchange Factor

PubMed Central

McDonald, Caleb B.; Bhat, Vikas; Kurouski, Dmitry; Mikles, David C.; Deegan, Brian J.; Seldeen, Kenneth L.; Lednev, Igor K.; Farooq, Amjad

2013-01-01

Despite its key role in mediating a plethora of cellular signaling cascades pertinent to health and disease, little is known about the structural landscape of the proline-rich (PR) domain of Sos1 guanine nucleotide exchange factor. Herein, using a battery of biophysical tools, we provide evidence that the PR domain of Sos1 is structurally disordered and adopts an extended random coil-like conformation in solution. Of particular interest is the observation that while chemical denaturation of PR domain results in the formation of a significant amount of polyproline II (PPII) helices, it has little or negligible effect on its overall size as measured by its hydrodynamic radius. Our data also show that the PR domain displays a highly dynamic conformational basin in agreement with the knowledge that the intrinsically unstructured proteins rapidly interconvert between an ensemble of conformations. Collectively, our study provides new insights into the conformational equilibrium of a key signaling molecule with important consequences on its physiological function. PMID:23528987

A FYVE zinc finger domain protein specifically links mRNA transport to endosome trafficking.

PubMed

Pohlmann, Thomas; Baumann, Sebastian; Haag, Carl; Albrecht, Mario; Feldbrügge, Michael

2015-05-18

An emerging theme in cellular logistics is the close connection between mRNA and membrane trafficking. A prominent example is the microtubule-dependent transport of mRNAs and associated ribosomes on endosomes. This coordinated process is crucial for correct septin filamentation and efficient growth of polarised cells, such as fungal hyphae. Despite detailed knowledge on the key RNA-binding protein and the molecular motors involved, it is unclear how mRNAs are connected to membranes during transport. Here, we identify a novel factor containing a FYVE zinc finger domain for interaction with endosomal lipids and a new PAM2-like domain required for interaction with the MLLE domain of the key RNA-binding protein. Consistently, loss of this FYVE domain protein leads to specific defects in mRNA, ribosome, and septin transport without affecting general functions of endosomes or their movement. Hence, this is the first endosomal component specific for mRNP trafficking uncovering a new mechanism to couple mRNPs to endosomes.

Testing domain general learning in an Australian lizard.

PubMed

Qi, Yin; Noble, Daniel W A; Fu, Jinzhong; Whiting, Martin J

2018-06-02

A key question in cognition is whether animals that are proficient in a specific cognitive domain (domain specific hypothesis), such as spatial learning, are also proficient in other domains (domain general hypothesis) or whether there is a trade-off. Studies testing among these hypotheses are biased towards mammals and birds. To understand constraints on the evolution of cognition more generally, we need broader taxonomic and phylogenetic coverage. We used Australian eastern water skinks (Eulamprus quoyii) with known spatial learning ability in three additional tasks: an instrumental and two discrimination tasks. Under domain specific learning we predicted that lizards that were good at spatial learning would perform less well in the discrimination tasks. Conversely, we predicted that lizards that did not meet our criterion for spatial learning would likewise perform better in discrimination tasks. Lizards with domain general learning should perform approximately equally well (or poorly) in these tasks. Lizards classified as spatial learners performed no differently to non-spatial learners in both the instrumental and discrimination learning tasks. Nevertheless, lizards were proficient in all tasks. Our results reveal two patterns: domain general learning in spatial learners and domain specific learning in non-spatial learners. We suggest that delineating learning into domain general and domain specific may be overly simplistic and we need to instead focus on individual variation in learning ability, which ultimately, is likely to play a key role in fitness. These results, in combination with previously published work on this species, suggests that this species has behavioral flexibility because they are competent across multiple cognitive domains and are capable of reversal learning.

Spectral Filtering Criteria for U-Band Test Light for In-Service Line Monitoring in Optical Fiber Networks

NASA Astrophysics Data System (ADS)

Honda, Nazuki; Izumita, Hisashi; Nakamura, Minoru

2006-06-01

In the fiber-to-the-home era, thousands of optical fibers will have to be accommodated in the central offices of optical access networks. To reduce maintenance costs and improve the service reliability of optical fiber networks, the authors must develop an optical fiber line testing system with a function for in-service line monitoring that uses a test light with a wavelength different from the communication light wavelength. To monitor an in-service line in an optical network, the effective rejection ratio of the test light must be taken into account. This ratio depends on the spectrum of the test light from the optical time-domain reflectometer and the rejection band of the filter in front of the optical network unit. The dependence of the effective rejection ratio as a function of the sideband suppression ratio (SBSR) and of the ratio of the rejection band to the bandwidth of the sideband noise d/D is clarified. When d/D =0.1 and the target effective rejection ratio of the filter is -40 dB, the SBSR and the filter loss of the termination cable must be -70 and -43 dB, respectively, or the SBSR must be -80 dB. When d/D < 0.5 and the target effective rejection ratio of the filter is -40 dB, the SBSR is also required to be -80 dB. In-service line monitoring for a 10-Gb/s transmission using a 1650-nm test light with an SBSR of -80 dB is also demonstrated.

Approaches to Learning and School Readiness in Head Start: Applications to Preschool Science

ERIC Educational Resources Information Center

Bustamante, Andres S.; White, Lisa J.; Greenfield, Daryl B.

2017-01-01

Approaches to learning are a set of domain-general skills that encompass curiosity, persistence, planning, and engagement in group learning. These skills play a key role in preschoolers' learning and predict school readiness in math and language. Preschool science is a critical domain for early education and facilitates learning across domains.…

The at-wavelength metrology facility for UV- and XUV-reflection and diffraction optics at BESSY-II

PubMed Central

Schäfers, F.; Bischoff, P.; Eggenstein, F.; Erko, A.; Gaupp, A.; Künstner, S.; Mast, M.; Schmidt, J.-S.; Senf, F.; Siewert, F.; Sokolov, A.; Zeschke, Th.

2016-01-01

A technology center for the production of high-precision reflection gratings has been established. Within this project a new optics beamline and a versatile reflectometer for at-wavelength characterization of UV- and XUV-reflection gratings and other (nano-) optical elements has been set up at BESSY-II. The Plane Grating Monochromator beamline operated in collimated light (c-PGM) is equipped with an SX700 monochromator, of which the blazed gratings (600 and 1200 lines mm−1) have been recently exchanged for new ones of improved performance produced in-house. Over the operating range from 10 to 2000 eV this beamline has very high spectral purity achieved by (i) a four-mirror arrangement of different coatings which can be inserted into the beam at different angles and (ii) by absorber filters for high-order suppression. Stray light and scattered radiation is removed efficiently by double sets of in situ exchangeable apertures and slits. By use of in- and off-plane bending-magnet radiation the beamline can be adjusted to either linear or elliptical polarization. One of the main features of a novel 11-axes reflectometer is the possibility to incorporate real life-sized gratings. The samples are adjustable within six degrees of freedom by a newly developed UHV-tripod system carrying a load up to 4 kg, and the reflectivity can be measured between 0 and 90° incidence angle for both s- and p-polarization geometry. This novel powerful metrology facility has gone into operation recently and is now open for external users. First results on optical performance and measurements on multilayer gratings will be presented here. PMID:26698047

Use of different surface analysis techniques for the study of the photo-degradation of a polymeric matrix composite

NASA Astrophysics Data System (ADS)

Larena, A.; Ochoa, S. Jimenez de

2004-11-01

Polypropylene matrix composites, with different reinforcement degrees of long glass fibres, are usually used in different fields of the industry, like aeronautics or automotive. Owed to their huge application field, and work under diverse and severe conditions, samples of the materials were exposed to artificial accelerated photo ageing in UV chamber (Heraeus Xenotest 15OS). Although the oxidative mechanism of the PP is known enough, the fact that the material presents a high content of glass fibre, cause a surface degradation higher than that the case of no reinforced materials, owed to the presence of the fibres near the surface. In order to study this topographic modifications, the optical confocal microscopy is used that allows us the analysis of the material surface with more accuracy than a surface profiler, and with nanometric precision. We also want a correlation between surface degradation studied by confocal microscopy and reflectometer measurements. By this way, we can know the surface state, and the degradation evolution, by means of a set of easy measurements, taken with a portable reflectometer, in samples at work, without preparation. Since these materials shall fulfil some aesthetic requirements, we study also, by means of UV-vis spectroscopy, Yellow Index and White Index variations, trying to explain the photochemical processes causing these modifications. Also, the fact that these materials are usually subjected to surface treatments like adhesion or painting makes necessary the study of surface energy. We study the variation of this factor with exposing time and percentage of fibre, by means of contact angle measurements, with different liquids of known surface tensions.

High Resolution Millimeter Wave Inspecting of the Orbiter Acreage Heat Tiles of the Space Shuttle

NASA Technical Reports Server (NTRS)

Case, J. T.; Khakovsky, S.; Zoughi, r.; Hepburn, F.

2007-01-01

Presence of defects such as disbonds, delaminations, impact damage, in thermal protection systems can significantly reduce safety of the Space Shuttle and its crew. The physical cause of Space Shuttle Columbia's catastrophic failure was a breach in its thermal protection system, caused by a piece of external tank insulating foam separating from the external tank and striking the leading edge of the left wing of the orbiter. There is an urgent need for a rapid, robust and life-circle oriented nondestructive testing (NDT) technique capable of inspecting the external tank insulating foam as well as the orbiter's protective (acreage) heat tiles and its fuselage prior and subsequent to a launch. Such a comprehensive inspection technique enables NASA to perform life-cycle inspection on critical components of the orbiter and its supporting hardware. Consequently, NASA Marshall Space Flight Center initiated an investigation into several potentially viable NDT techniques for this purpose. Microwave and millimeter wave NDT methods have shown great potential to achieve these goals. These methods have been successfully used to produce images of the interior of various complex, thick and thin external tank insulating foam structures for real focused reflectometer at operating frequency from 50-100 GHz and for synthetic aperture techniques at Ku-band (12-18 GHz) and K-band (18-26 GHz). Preliminary results of inspecting heat tile specimens show that increasing resolution of the measurement system is an important issue. This paper presents recent results of an investigation for the purpose of detecting anomalies such as debonds and corrosion in metal substrate in complex multi-sectioned protective heat tile specimens using a real focused 150 GHz (D-band) reflectometer and wide-band millimeter wave holography at 33-50, GHz (Q-band).

Calibrating electromagnetic induction conductivities with time-domain reflectometry measurements

NASA Astrophysics Data System (ADS)

Dragonetti, Giovanna; Comegna, Alessandro; Ajeel, Ali; Piero Deidda, Gian; Lamaddalena, Nicola; Rodriguez, Giuseppe; Vignoli, Giulio; Coppola, Antonio

2018-02-01

This paper deals with the issue of monitoring the spatial distribution of bulk electrical conductivity, σb, in the soil root zone by using electromagnetic induction (EMI) sensors under different water and salinity conditions. To deduce the actual distribution of depth-specific σb from EMI apparent electrical conductivity (ECa) measurements, we inverted the data by using a regularized 1-D inversion procedure designed to manage nonlinear multiple EMI-depth responses. The inversion technique is based on the coupling of the damped Gauss-Newton method with truncated generalized singular value decomposition (TGSVD). The ill-posedness of the EMI data inversion is addressed by using a sharp stabilizer term in the objective function. This specific stabilizer promotes the reconstruction of blocky targets, thereby contributing to enhance the spatial resolution of the EMI results in the presence of sharp boundaries (otherwise smeared out after the application of more standard Occam-like regularization strategies searching for smooth solutions). Time-domain reflectometry (TDR) data are used as ground-truth data for calibration of the inversion results. An experimental field was divided into four transects 30 m long and 2.8 m wide, cultivated with green bean, and irrigated with water at two different salinity levels and using two different irrigation volumes. Clearly, this induces different salinity and water contents within the soil profiles. For each transect, 26 regularly spaced monitoring soundings (1 m apart) were selected for the collection of (i) Geonics EM-38 and (ii) Tektronix reflectometer data. Despite the original discrepancies in the EMI and TDR data, we found a significant correlation of the means and standard deviations of the two data series; in particular, after a low-pass spatial filtering of the TDR data. Based on these findings, this paper introduces a novel methodology to calibrate EMI-based electrical conductivities via TDR direct measurements. This calibration strategy consists of a linear mapping of the original inversion results into a new conductivity spatial distribution with the coefficients of the transformation uniquely based on the statistics of the two original measurement datasets (EMI and TDR conductivities).

Switching Cyclic Nucleotide-Selective Activation of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Holoenzyme Reveals Distinct Roles of Tandem Cyclic Nucleotide-Binding Domains.

PubMed

He, Daniel; Lorenz, Robin; Kim, Choel; Herberg, Friedrich W; Lim, Chinten James

2017-12-15

The cyclic adenosine monophosphate (cAMP)- and cyclic guanosine monophosphate (cGMP)-dependent protein kinases (PKA and PKG) are key effectors of cyclic nucleotide signaling. Both share structural features that include tandem cyclic nucleotide-binding (CNB) domains, CNB-A and CNB-B, yet their functions are separated through preferential activation by either cAMP or cGMP. Based on structural studies and modeling, key CNB contact residues have been identified for both kinases. In this study, we explored the requirements for conversion of PKA activation from cAMP-dependent to cGMP-dependent. The consequences of the residue substitutions T192R/A212T within CNB-A or G316R/A336T within CNB-B of PKA-RIα on cyclic nucleotide binding and holoenzyme activation were assessed in vitro using purified recombinant proteins, and ex vivo using RIα-deficient mouse embryonic fibroblasts genetically reconstituted with wild-type or mutant PKA-RIα. In vitro, a loss of binding and activation selectivity was observed when residues in either one of the CNB domains were mutated, while mutations in both CNB domains resulted in a complete switch of selectivity from cAMP to cGMP. The switch in selectivity was also recapitulated ex vivo, confirming their functional roles in cells. Our results highlight the importance of key cyclic nucleotide contacts within each CNB domain and suggest that these domains may have evolved from an ancestral gene product to yield two distinct cyclic nucleotide-dependent protein kinases.

Reflections of Science Teachers in a Professional Development Intervention to Improve Their Ability to Teach for the Affective Domain

ERIC Educational Resources Information Center

Buma, Anastasia Malong

2018-01-01

This paper reports on key aspects of a short in-service programme improving science teachers' pedagogical content knowledge to teach for the affective domain. The affective domain refers to outcomes that involve changes in feelings, values, appreciation, interests, motivations or attitudes that might result from a learning experience. The…

Color image encryption by using Yang-Gu mixture amplitude-phase retrieval algorithm in gyrator transform domain and two-dimensional Sine logistic modulation map

NASA Astrophysics Data System (ADS)

Sui, Liansheng; Liu, Benqing; Wang, Qiang; Li, Ye; Liang, Junli

2015-12-01

A color image encryption scheme is proposed based on Yang-Gu mixture amplitude-phase retrieval algorithm and two-coupled logistic map in gyrator transform domain. First, the color plaintext image is decomposed into red, green and blue components, which are scrambled individually by three random sequences generated by using the two-dimensional Sine logistic modulation map. Second, each scrambled component is encrypted into a real-valued function with stationary white noise distribution in the iterative amplitude-phase retrieval process in the gyrator transform domain, and then three obtained functions are considered as red, green and blue channels to form the color ciphertext image. Obviously, the ciphertext image is real-valued function and more convenient for storing and transmitting. In the encryption and decryption processes, the chaotic random phase mask generated based on logistic map is employed as the phase key, which means that only the initial values are used as private key and the cryptosystem has high convenience on key management. Meanwhile, the security of the cryptosystem is enhanced greatly because of high sensitivity of the private keys. Simulation results are presented to prove the security and robustness of the proposed scheme.

A FYVE zinc finger domain protein specifically links mRNA transport to endosome trafficking

PubMed Central

Pohlmann, Thomas; Baumann, Sebastian; Haag, Carl; Albrecht, Mario; Feldbrügge, Michael

2015-01-01

An emerging theme in cellular logistics is the close connection between mRNA and membrane trafficking. A prominent example is the microtubule-dependent transport of mRNAs and associated ribosomes on endosomes. This coordinated process is crucial for correct septin filamentation and efficient growth of polarised cells, such as fungal hyphae. Despite detailed knowledge on the key RNA-binding protein and the molecular motors involved, it is unclear how mRNAs are connected to membranes during transport. Here, we identify a novel factor containing a FYVE zinc finger domain for interaction with endosomal lipids and a new PAM2-like domain required for interaction with the MLLE domain of the key RNA-binding protein. Consistently, loss of this FYVE domain protein leads to specific defects in mRNA, ribosome, and septin transport without affecting general functions of endosomes or their movement. Hence, this is the first endosomal component specific for mRNP trafficking uncovering a new mechanism to couple mRNPs to endosomes. DOI: http://dx.doi.org/10.7554/eLife.06041.001 PMID:25985087

Structural landscape of the proline-rich domain of Sos1 nucleotide exchange factor.

PubMed

McDonald, Caleb B; Bhat, Vikas; Kurouski, Dmitry; Mikles, David C; Deegan, Brian J; Seldeen, Kenneth L; Lednev, Igor K; Farooq, Amjad

2013-01-01

Despite its key role in mediating a plethora of cellular signaling cascades pertinent to health and disease, little is known about the structural landscape of the proline-rich (PR) domain of Sos1 guanine nucleotide exchange factor. Herein, using a battery of biophysical tools, we provide evidence that the PR domain of Sos1 is structurally disordered and adopts an extended random coil-like conformation in solution. Of particular interest is the observation that while chemical denaturation of PR domain results in the formation of a significant amount of polyproline II (PPII) helices, it has little or negligible effect on its overall size as measured by its hydrodynamic radius. Our data also show that the PR domain displays a highly dynamic conformational basin in agreement with the knowledge that the intrinsically unstructured proteins rapidly interconvert between an ensemble of conformations. Collectively, our study provides new insights into the conformational equilibrium of a key signaling molecule with important consequences on its physiological function. Copyright © 2013 Elsevier B.V. All rights reserved.

Autophagic Regulation of p62 is Critical for Cancer Therapy

PubMed Central

Islam, Md. Ariful; Sooro, Mopa Alina

2018-01-01

Sequestosome1 (p62/SQSTM 1) is a multidomain protein that interacts with the autophagy machinery as a key adaptor of target cargo. It interacts with phagophores through the LC3-interacting (LIR) domain and with the ubiquitinated protein aggregates through the ubiquitin-associated domain (UBA) domain. It sequesters the target cargo into inclusion bodies by its PB1 domain. This protein is further the central hub that interacts with several key signaling proteins. Emerging evidence implicates p62 in the induction of multiple cellular oncogenic transformations. Indeed, p62 upregulation and/or reduced degradation have been implicated in tumor formation, cancer promotion as well as in resistance to therapy. It has been established that the process of autophagy regulates the levels of p62. Autophagy-dependent apoptotic activity of p62 is recently being reported. It is evident that p62 plays a critical role in both autophagy and apoptosis. Therefore in this review we discuss the role of p62 in autophagy, apoptosis and cancer through its different domains and outline the importance of modulating cellular levels of p62 in cancer therapeutics. PMID:29738493

Autophagic Regulation of p62 is Critical for Cancer Therapy.

PubMed

Islam, Md Ariful; Sooro, Mopa Alina; Zhang, Pinghu

2018-05-08

Sequestosome1 (p62/SQSTM 1) is a multidomain protein that interacts with the autophagy machinery as a key adaptor of target cargo. It interacts with phagophores through the LC3-interacting (LIR) domain and with the ubiquitinated protein aggregates through the ubiquitin-associated domain (UBA) domain. It sequesters the target cargo into inclusion bodies by its PB1 domain. This protein is further the central hub that interacts with several key signaling proteins. Emerging evidence implicates p62 in the induction of multiple cellular oncogenic transformations. Indeed, p62 upregulation and/or reduced degradation have been implicated in tumor formation, cancer promotion as well as in resistance to therapy. It has been established that the process of autophagy regulates the levels of p62. Autophagy-dependent apoptotic activity of p62 is recently being reported. It is evident that p62 plays a critical role in both autophagy and apoptosis. Therefore in this review we discuss the role of p62 in autophagy, apoptosis and cancer through its different domains and outline the importance of modulating cellular levels of p62 in cancer therapeutics.

Domains of quality of life: results of a three-stage Delphi consensus procedure among patients, family of patients, clinicians, scientists and the general public.

PubMed

Pietersma, Suzanne; de Vries, Marieke; van den Akker-van Marle, M Elske

2014-06-01

Our key objective is to identify the core domains of health-related quality of life (QoL). Health-related QoL utility scales are commonly used in economic evaluations to assess the effectiveness of health-care interventions. However, health-care interventions are likely to affect QoL in a broader sense than is quantifiable with traditional scales. Therefore, measures need to go beyond these scales. Unfortunately, there is no consensus in the scientific literature on the essential domains of QoL. We conducted a three-stage online Delphi consensus procedure to identify the key domains of health-related QoL. Five stakeholder groups (i.e., patients, family of patients, clinicians, scientists and general public) were asked, on three consecutive occasions, what they perceive as the most important domains of health-related QoL. An analysis of existing (health-related) QoL and well-being measurements formed the basis of the Delphi-procedure. In total, 42 domains of QoL were judged, covering physical, mental and social aspects. All participants rated 'self-acceptance', 'self-esteem' and 'good social contacts' as essential. Strikingly, mental and social domains are perceived as more essential than physical domains across stakeholders groups. In traditionally used health-related QoL utility measures, physical domains like 'mobility' are prominently present. The Delphi-procedure shows that health-related QoL (utility) scales need to put sufficient emphasis on mental and social domains to capture aspects of QoL that are essential to people.

The reflectance of Ames 24E, Infrablack, and Martin black. [anodizing coatings for far-infrared space telescopes

NASA Technical Reports Server (NTRS)

Smith, Sheldon M.

1989-01-01

Results are reported from measurements of the specular reflectances (SRs) and bidirectional reflectance distribution functions (BRDFs) of three black optical coatings in the FIR wavelength range. The nonspecular reflectometer apparatus described by Smith (1984) is employed, and the data are presented in tables and graphs and discussed in detail. It is found that Ames 24E has an FIR SR one order of magnitude lower than that of Martin black (MB), with BRDF values characteristic of a nearly Lambertian surface, while Infrablack has SR two orders lower than MB and a specular-diffuse surface; MB itself has a very specular surface.

Spectral infrared hemispherical reflectance measurements for LDEF tray clamps

NASA Technical Reports Server (NTRS)

Cromwell, B. K.; Shepherd, S. D.; Pender, C. W.; Wood, B. E.

1993-01-01

Infrared hemispherical reflectance measurements that were made on 58 chromic acid anodized tray clamps from LDEF are described. The measurements were made using a hemiellipsoidal mirror reflectometer with interferometer for wavelengths between 2-15 microns. The tray clamps investigated were from locations about the entire spacecraft and provided the opportunity for comparing the effects of atomic oxygen at each location. Results indicate there was essentially no dependence on atomic oxygen fluence for the surfaces studied, but there did appear to be a slight dependence on solar radiation exposure. The reflectances of the front sides of the tray clamps consistently were slightly higher than for the protected rear tray clamp surfaces.

Quality of dry chemistry testing.

PubMed

Nakamura, H; Tatsumi, N

1999-01-01

Since the development of the qualitative test paper for urine in 1950s, several kinds of dry-state-reagents and their automated analyzers have been developed. "Dry chemistry" has become to be called since the report on the development of quantitative test paper for serum bilirubin with reflectometer in the end of 1960s and dry chemistry has been world widely known since the presentation on the development of multilayer film reagent for serum biochemical analytes by Eastman Kodak Co at the 10th IFCC Meeting in the end of 1970s. We have reported test menu, results in external quality assessment, merits and demerits, and the future possibilities of dry chemistry.

Performance assessment of geotechnical structural elements using distributed fiber optic sensing

NASA Astrophysics Data System (ADS)

Monsberger, Christoph; Woschitz, Helmut; Lienhart, Werner; Račanský, Václav; Hayden, Martin

2017-04-01

Geotechnical structural elements are used to underpin heavy structures or to stabilize slopes and embankments. The bearing capacity of these components is usually verified by geotechnical load tests. It is state of the art to measure the resulting deformations with electronic sensors at the surface and therefore, the load distribution along the objects cannot be determined. This paper reports about distributed strain measurements with an optical backscatter reflectometer along geotechnical elements. In addition to the installation of the optical fiber in harsh field conditions, results of investigations of the fiber optic system in the laboratory and the most significant results of the field trials are presented.

An adaptive signal-processing approach to online adaptive tutoring.

PubMed

Bergeron, Bryan; Cline, Andrew

2011-01-01

Conventional intelligent or adaptive tutoring online systems rely on domain-specific models of learner behavior based on rules, deep domain knowledge, and other resource-intensive methods. We have developed and studied a domain-independent methodology of adaptive tutoring based on domain-independent signal-processing approaches that obviate the need for the construction of explicit expert and student models. A key advantage of our method over conventional approaches is a lower barrier to entry for educators who want to develop adaptive online learning materials.

Structural Characterization of Monomeric/Dimeric State of p59fyn SH2 Domain.

PubMed

Huculeci, Radu; Kieken, Fabien; Garcia-Pino, Abel; Buts, Lieven; van Nuland, Nico; Lenaerts, Tom

2017-01-01

Src homology 2 (SH2) domains are key modulators in various signaling pathways allowing the recognition of phosphotyrosine sites of different proteins. Despite the fact that SH2 domains acquire their biological functions in a monomeric state, a multitude of reports have shown their tendency to dimerize. Here, we provide a technical description on how to isolate and characterize by gel filtration, circular dichroism (CD), and nuclear magnetic resonance (NMR) each conformational state of p59 fyn SH2 domain.

Exceptionally tight membrane-binding may explain the key role of the synaptotagmin-7 C 2 A domain in asynchronous neurotransmitter release

DOE Office of Scientific and Technical Information (OSTI.GOV)

Voleti, Rashmi; Tomchick, Diana R.; Südhof, Thomas C.

Synaptotagmins (Syts) act as Ca2+ sensors in neurotransmitter release by virtue of Ca2+-binding to their two C2 domains, but their mechanisms of action remain unclear. Puzzlingly, Ca2+-binding to the C2B domain appears to dominate Syt1 function in synchronous release, whereas Ca2+-binding to the C2A domain mediates Syt7 function in asynchronous release. Here we show that crystal structures of the Syt7 C2A domain and C2AB region, and analyses of intrinsic Ca2+-binding to the Syt7 C2 domains using isothermal titration calorimetry, did not reveal major differences that could explain functional differentiation between Syt7 and Syt1. However, using liposome titrations under Ca2+ saturatingmore » conditions, we show that the Syt7 C2A domain has a very high membrane affinity and dominates phospholipid binding to Syt7 in the presence or absence of L-α-phosphatidylinositol 4,5-diphosphate (PIP2). For Syt1, the two Ca2+-saturated C2 domains have similar affinities for membranes lacking PIP2, but the C2B domain dominates binding to PIP2-containing membranes. Mutagenesis revealed that the dramatic differences in membrane affinity between the Syt1 and Syt7 C2A domains arise in part from apparently conservative residue substitutions, showing how striking biochemical and functional differences can result from the cumulative effects of subtle residue substitutions. Viewed together, our results suggest that membrane affinity may be a key determinant of the functions of Syt C2 domains in neurotransmitter release.« less

How to build a molecular shock absorber.

PubMed

McGough, A

1999-12-02

Newly determined structures of the alpha-helical repeats that make up the key 'rod' domains of spectrin and alpha-actinin - which serve as spacers between their actin-binding domains - have provided important insights into how these proteins function as molecular shock absorbers in cells.

Concept Mapping of PMTCT Implementation Challenges and Solutions Across 6 sub-Saharan African Countries in the NIH-PEPFAR PMTCT Implementation Science Alliance.

PubMed

Aarons, Gregory A; Sommerfeld, David H; Chi, Benjamin H; Ezeanolue, Echezona E; Sturke, Rachel; Guay, Laura; Siberry, George K

2016-08-01

Although tremendous gains have been made to reduce mother-to-child HIV transmission (MTCT) globally, evidence-based practice implementation remains inconsistent in sub-Saharan Africa. We sought to identify the key domains for effective prevention of MTCT (PMTCT) implementation, using a participatory mixed-methods approach. Participants were members of the NIH-PEPFAR PMTCT Implementation Science Alliance (ISA), a platform of researchers, public-health practitioners, policymakers, and donors supported through NIH/PEPFAR. We used concept mapping to identify priority areas for PMTCT implementation science. Participants responded to the focus question: "In your experience, what factors have facilitated or hindered implementation of PMTCT interventions?" Responses were consolidated into discrete statements, grouped together based on similarity, and rated for importance, changeability, and extent to which ISA participation enhanced the capacity to influence/change the factor. Using multidimensional scaling and cluster analysis, we identified 12 key domains of PMTCT implementation. Two domains (Governmental Commitment and Data Measurement & Collection) were consistently ranked at or near the top for overall importance, perceived changeability, and enhanced ability to address through ISA participation. Through a stakeholder-based, participatory approach, we identified key domains for that should be considered for future PMTCT implementation research in sub-Saharan Africa.

The nanoscale organization of signaling domains at the plasma membrane.

PubMed

Griffié, Juliette; Burn, Garth; Owen, Dylan M

2015-01-01

In this chapter, we present an overview of the role of the nanoscale organization of signaling domains in regulating key cellular processes. In particular, we illustrate the importance of protein and lipid nanodomains as triggers and mediators of cell signaling. As particular examples, we summarize the state of the art of understanding the role of nanodomains in the mounting of an immune response, cellular adhesion, intercellular communication, and cell proliferation. Thus, this chapter underlines the essential role the nanoscale organization of key signaling proteins and lipid domains. We will also see how nanodomains play an important role in the lifecycle of many pathogens relevant to human disease and therefore illustrate how these structures may become future therapeutic targets. Copyright © 2015 Elsevier Inc. All rights reserved.

CTLs, a new class of RING-H2 ubiquitin ligases uncovered by YEELL, a motif close to the RING domain that is present across eukaryotes.

PubMed

Jiménez-López, Domingo; Aguilar-Henonin, Laura; González-Prieto, Juan Manuel; Aguilar-Hernández, Victor; Guzmán, Plinio

2018-01-01

RING ubiquitin E3 ligases enclose a RING domain for ubiquitin ligase activity and associated domains and/or conserved motifs outside the RING domain that collectively facilitate their classification and usually reveal some of key information related to mechanism of action. Here we describe a new family of E3 ligases that encodes a RING-H2 domain related in sequence to the ATL and BTL RING-H2 domains. This family, named CTL, encodes a motif designed as YEELL that expands 21 amino acids next to the RING-H2 domain that is present across most eukaryotic lineages. E3 ubiquitin ligase BIG BROTHER is a plant CTL that regulates organ size, and SUMO-targeted ubiquitin E3 ligase RNF111/ARKADIA is a vertebrate CTL. Basal animal and vertebrate, as well as fungi species, encode a single CTL gene that constraints the number of paralogs observed in vertebrates. Conversely, as previously described in ATL and BTL families in plants, CTL genes range from a single copy in green algae and 3 to 5 copies in basal species to 9 to 35 copies in angiosperms. Our analysis describes key structural features of a novel family of E3 ubiquitin ligases as an integral component of the set of core eukaryotic genes.

Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling.

PubMed

D'Cruz, Akshay A; Kershaw, Nadia J; Chiang, Jessica J; Wang, May K; Nicola, Nicos A; Babon, Jeffrey J; Gack, Michaela U; Nicholson, Sandra E

2013-12-01

TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp(488) and Trp(621)) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs.

Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling

PubMed Central

D'Cruz, Akshay A.; Kershaw, Nadia J.; Chiang, Jessica J.; Wang, May K.; Nicola, Nicos A.; Babon, Jeffrey J.; Gack, Michaela U.; Nicholson, Sandra E.

2014-01-01

TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp488 and Trp621) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs. PMID:24015671

CTLs, a new class of RING-H2 ubiquitin ligases uncovered by YEELL, a motif close to the RING domain that is present across eukaryotes

PubMed Central

Jiménez-López, Domingo; Aguilar-Henonin, Laura; González-Prieto, Juan Manuel; Aguilar-Hernández, Victor

2018-01-01

RING ubiquitin E3 ligases enclose a RING domain for ubiquitin ligase activity and associated domains and/or conserved motifs outside the RING domain that collectively facilitate their classification and usually reveal some of key information related to mechanism of action. Here we describe a new family of E3 ligases that encodes a RING-H2 domain related in sequence to the ATL and BTL RING-H2 domains. This family, named CTL, encodes a motif designed as YEELL that expands 21 amino acids next to the RING-H2 domain that is present across most eukaryotic lineages. E3 ubiquitin ligase BIG BROTHER is a plant CTL that regulates organ size, and SUMO-targeted ubiquitin E3 ligase RNF111/ARKADIA is a vertebrate CTL. Basal animal and vertebrate, as well as fungi species, encode a single CTL gene that constraints the number of paralogs observed in vertebrates. Conversely, as previously described in ATL and BTL families in plants, CTL genes range from a single copy in green algae and 3 to 5 copies in basal species to 9 to 35 copies in angiosperms. Our analysis describes key structural features of a novel family of E3 ubiquitin ligases as an integral component of the set of core eukaryotic genes. PMID:29324855

Rift Valley fever phlebovirus NSs protein core domain structure suggests molecular basis for nuclear filaments

PubMed Central

Miller, Ona K; Potter, Jane A; Vijayakrishnan, Swetha; Bhella, David; Naismith, James H; Elliott, Richard M

2017-01-01

Rift Valley fever phlebovirus (RVFV) is a clinically and economically important pathogen increasingly likely to cause widespread epidemics. RVFV virulence depends on the interferon antagonist non-structural protein (NSs), which remains poorly characterized. We identified a stable core domain of RVFV NSs (residues 83–248), and solved its crystal structure, a novel all-helical fold organized into highly ordered fibrils. A hallmark of RVFV pathology is NSs filament formation in infected cell nuclei. Recombinant virus encoding the NSs core domain induced intranuclear filaments, suggesting it contains all essential determinants for nuclear translocation and filament formation. Mutations of key crystal fibril interface residues in viruses encoding full-length NSs completely abrogated intranuclear filament formation in infected cells. We propose the fibrillar arrangement of the NSs core domain in crystals reveals the molecular basis of assembly of this key virulence factor in cell nuclei. Our findings have important implications for fundamental understanding of RVFV virulence. PMID:28915104

Rift Valley fever phlebovirus NSs protein core domain structure suggests molecular basis for nuclear filaments.

PubMed

Barski, Michal; Brennan, Benjamin; Miller, Ona K; Potter, Jane A; Vijayakrishnan, Swetha; Bhella, David; Naismith, James H; Elliott, Richard M; Schwarz-Linek, Ulrich

2017-09-15

Rift Valley fever phlebovirus (RVFV) is a clinically and economically important pathogen increasingly likely to cause widespread epidemics. RVFV virulence depends on the interferon antagonist non-structural protein (NSs), which remains poorly characterized. We identified a stable core domain of RVFV NSs (residues 83-248), and solved its crystal structure, a novel all-helical fold organized into highly ordered fibrils. A hallmark of RVFV pathology is NSs filament formation in infected cell nuclei. Recombinant virus encoding the NSs core domain induced intranuclear filaments, suggesting it contains all essential determinants for nuclear translocation and filament formation. Mutations of key crystal fibril interface residues in viruses encoding full-length NSs completely abrogated intranuclear filament formation in infected cells. We propose the fibrillar arrangement of the NSs core domain in crystals reveals the molecular basis of assembly of this key virulence factor in cell nuclei. Our findings have important implications for fundamental understanding of RVFV virulence.

Disruptions of network connectivity predict impairment in multiple behavioral domains after stroke

PubMed Central

Ramsey, Lenny E.; Metcalf, Nicholas V.; Chacko, Ravi V.; Weinberger, Kilian; Baldassarre, Antonello; Hacker, Carl D.; Shulman, Gordon L.; Corbetta, Maurizio

2016-01-01

Deficits following stroke are classically attributed to focal damage, but recent evidence suggests a key role of distributed brain network disruption. We measured resting functional connectivity (FC), lesion topography, and behavior in multiple domains (attention, visual memory, verbal memory, language, motor, and visual) in a cohort of 132 stroke patients, and used machine-learning models to predict neurological impairment in individual subjects. We found that visual memory and verbal memory were better predicted by FC, whereas visual and motor impairments were better predicted by lesion topography. Attention and language deficits were well predicted by both. Next, we identified a general pattern of physiological network dysfunction consisting of decrease of interhemispheric integration and intrahemispheric segregation, which strongly related to behavioral impairment in multiple domains. Network-specific patterns of dysfunction predicted specific behavioral deficits, and loss of interhemispheric communication across a set of regions was associated with impairment across multiple behavioral domains. These results link key organizational features of brain networks to brain–behavior relationships in stroke. PMID:27402738

Aggregation of γ-crystallins associated with human cataracts via domain swapping at the C-terminal β-strands

PubMed Central

Das, Payel; King, Jonathan A.; Zhou, Ruhong

2011-01-01

The prevalent eye disease age-onset cataract is associated with aggregation of human γD-crystallins, one of the longest-lived proteins. Identification of the γ-crystallin precursors to aggregates is crucial for developing strategies to prevent and reverse cataract. Our microseconds of atomistic molecular dynamics simulations uncover the molecular structure of the experimentally detected aggregation-prone folding intermediate species of monomeric native γD-crystallin with a largely folded C-terminal domain and a mostly unfolded N-terminal domain. About 30 residues including a, b, and c strands from the Greek Key motif 4 of the C-terminal domain experience strong solvent exposure of hydrophobic residues as well as partial unstructuring upon N-terminal domain unfolding. Those strands comprise the domain–domain interface crucial for unusually high stability of γD-crystallin. We further simulate the intermolecular linkage of these monomeric aggregation precursors, which reveals domain-swapped dimeric structures. In the simulated dimeric structures, the N-terminal domain of one monomer is frequently found in contact with residues 135–164 encompassing the a, b, and c strands of the Greek Key motif 4 of the second molecule. The present results suggest that γD-crystallin may polymerize through successive domain swapping of those three C-terminal β-strands leading to age-onset cataract, as an evolutionary cost of its very high stability. Alanine substitutions of the hydrophobic residues in those aggregation-prone β-strands, such as L145 and M147, hinder domain swapping as a pathway toward dimerization. These findings thus provide critical molecular insights onto the initial stages of age-onset cataract, which is important for understanding protein aggregation diseases. PMID:21670251

A Unified Approach to Intra-Domain Security

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shue, Craig A; Kalafut, Andrew J.; Gupta, Prof. Minaxi

2009-01-01

While a variety of mechanisms have been developed for securing individual intra-domain protocols, none address the issue in a holistic manner. We develop a unified framework to secure prominent networking protocols within a single domain. We begin with a secure version of the DHCP protocol, which has the additional feature of providing each host with a certificate. We then leverage these certificates to secure ARP, prevent spoofing within the domain, and secure SSH and VPN connections between the domain and hosts which have previously interacted with it locally. In doing so, we also develop an incrementally deployable public key infrastructuremore » which can later be leveraged to support inter-domain authentication.« less

Analysis of Coaxial Soil Cell in Reflection and Transmission

PubMed Central

Pelletier, Mathew G.; Viera, Joseph A.; Schwartz, Robert C.; Evett, Steven R.; Lascano, Robert J.; McMichael, Robert L.

2011-01-01

Accurate measurement of moisture content is a prime requirement in hydrological, geophysical and biogeochemical research as well as for material characterization and process control. Within these areas, accurate measurements of the surface area and bound water content is becoming increasingly important for providing answers to many fundamental questions ranging from characterization of cotton fiber maturity, to accurate characterization of soil water content in soil water conservation research to bio-plant water utilization to chemical reactions and diffusions of ionic species across membranes in cells as well as in the dense suspensions that occur in surface films. In these bound water materials, the errors in the traditional time-domain-reflectometer, “TDR”, exceed the range of the full span of the material’s permittivity that is being measured. Thus, there is a critical need to re-examine the TDR system and identify where the errors are to direct future research. One promising technique to address the increasing demands for higher accuracy water content measurements is utilization of electrical permittivity characterization of materials. This technique has enjoyed a strong following in the soil-science and geological community through measurements of apparent permittivity via time-domain-reflectometery as well in many process control applications. Recent research however, is indicating a need to increase the accuracy beyond that available from traditional TDR. The most logical pathway then becomes a transition from TDR based measurements to network analyzer measurements of absolute permittivity that will remove the adverse effects that high surface area soils and conductivity impart onto the measurements of apparent permittivity in traditional TDR applications. This research examines the theoretical basis behind the coaxial probe, from which the modern TDR probe originated from, to provide a basis on which to perform absolute permittivity measurements. The research reveals currently utilized formulations in accepted techniques for permittivity measurements which violate the underlying assumptions inherent in the basic models due to the TDR acting as an antenna by radiating energy off the end of the probe, rather than returning it back to the source as is the current assumption. To remove the effects of radiation from the experimental results obtain herein, this research utilized custom designed coaxial probes of various diameters and probe lengths by which to test the coaxial cell measurement technique for accuracy in determination of absolute permittivity. In doing so, the research reveals that the basic models available in the literature all omitted a key correction factor that is hypothesized by this research as being most likely due to fringe capacitance. To test this theory, a Poisson model of a coaxial cell was formulated to calculate the effective extra length provided by the fringe capacitance which is then used to correct the experimental results such that experimental measurements utilizing differing coaxial cell diameters and probe lengths, upon correction with the Poisson model derived correction factor, all produce the same results thereby lending support for the use of an augmented measurement technique, described herein, for measurement of absolute permittivity, as opposed to the traditional TDR measurement of apparent permittivity. PMID:22163757

Fast tracking the design of theory-based KT interventions through a consensus process.

PubMed

Bussières, André E; Al Zoubi, Fadi; Quon, Jeffrey A; Ahmed, Sara; Thomas, Aliki; Stuber, Kent; Sajko, Sandy; French, Simon

2015-02-11

Despite available evidence for optimal management of spinal pain, poor adherence to guidelines and wide variations in healthcare services persist. One of the objectives of the Canadian Chiropractic Guideline Initiative is to develop and evaluate targeted theory- and evidence-informed interventions to improve the management of non-specific neck pain by chiropractors. In order to systematically develop a knowledge translation (KT) intervention underpinned by the Theoretical Domains Framework (TDF), we explored the factors perceived to influence the use of multimodal care to manage non-specific neck pain, and mapped behaviour change techniques to key theoretical domains. Individual telephone interviews exploring beliefs about managing neck pain were conducted with a purposive sample of 13 chiropractors. The interview guide was based upon the TDF. Interviews were digitally recorded, transcribed verbatim and analysed by two independent assessors using thematic content analysis. A 15-member expert panel formally met to design a KT intervention. Nine TDF domains were identified as likely relevant. Key beliefs (and relevant domains of the TDF) included the following: influence of formal training, colleagues and patients on clinicians (Social Influences); availability of educational material (Environmental Context and Resources); and better clinical outcomes reinforcing the use of multimodal care (Reinforcement). Facilitating factors considered important included better communication (Skills); audits of patients' treatment-related outcomes (Behavioural Regulation); awareness and agreement with guidelines (Knowledge); and tailoring of multimodal care (Memory, Attention and Decision Processes). Clinicians conveyed conflicting beliefs about perceived threats to professional autonomy (Social/Professional Role and Identity) and speed of recovery from either applying or ignoring the practice recommendations (Beliefs about Consequences). The expert panel mapped behaviour change techniques to key theoretical domains and identified relevant KT strategies and modes of delivery to increase the use of multimodal care among chiropractors. A multifaceted KT educational intervention targeting chiropractors' management of neck pain was developed. The KT intervention consisted of an online education webinar series, clinical vignettes and a video underpinned by the Brief Action Planning model. The intervention was designed to reflect key theoretical domains, behaviour change techniques and intervention components. The effectiveness of the proposed intervention remains to be tested.

[Spatial heterogeneity of soil moisture of mountain apple orchards with rainwater collection and infiltration (RWCI) system in the Loess Plateau, China].

PubMed

Song, Xiao Lin; Zhao, Xi Ning; Gao, Xiao Dong; Wu, Pu Te; Ma, Wen; Yao, Jie; Jiang, Xiao Li; Zhang, Wei

2017-11-01

Water scarcity is a critical factor influencing rain-fed agricultural production on the Loess Plateau, and the exploitation of rainwater is an effective avenue to alleviate water scarcity in this area. This study was conducted to investigate the spatial and temporal distribution of soil moisture in the 0-300 cm under a 21-year-old apple orchard with the rainwater collection and infiltration (RWCI) system by using a time domain reflectometer (TDR) probe on the Loess Plateau. The results showed that there was a low soil moisture zone in the 40-80 cm under the CK, and the RWCI system significantly increased soil moisture in this depth interval. Over this depth, the annual average soil moisture under RWCI 40 , RWCI 60 and RWCI 80 was 39.2%, 47.2% and 29.1% higher than that of bare slope (BS) and 75.3%, 85.4% and 62.7% higher than that of CK, respectively. The maximum infiltration depth of water under RWCI 40 , RWCI 60 and RWCI 80 was 80 cm, 120 cm and 180 cm, respectively, and the soil moisture in the 0-60, 0-100 and 0-120 cm was more affected by RWCI 40 , RWCI 60 and RWCI 80 , respectively. Over the whole growth period of apple tree, the maximum value of soil moisture content in the 0-300 cm existed in the RWCI 80 treatment, followed by the RWCI 40 and RWCI 60 treatments. Overall, the RWCI system is an effective meaning of transforming rainwater to available water resources and realizing efficient use of agricultural water on the Loess Plateau.

S-Genius, a universal software platform with versatile inverse problem resolution for scatterometry

NASA Astrophysics Data System (ADS)

Fuard, David; Troscompt, Nicolas; El Kalyoubi, Ismael; Soulan, Sébastien; Besacier, Maxime

2013-05-01

S-Genius is a new universal scatterometry platform, which gathers all the LTM-CNRS know-how regarding the rigorous electromagnetic computation and several inverse problem solver solutions. This software platform is built to be a userfriendly, light, swift, accurate, user-oriented scatterometry tool, compatible with any ellipsometric measurements to fit and any types of pattern. It aims to combine a set of inverse problem solver capabilities — via adapted Levenberg- Marquard optimization, Kriging, Neural Network solutions — that greatly improve the reliability and the velocity of the solution determination. Furthermore, as the model solution is mainly vulnerable to materials optical properties, S-Genius may be coupled with an innovative material refractive indices determination. This paper will a little bit more focuses on the modified Levenberg-Marquardt optimization, one of the indirect method solver built up in parallel with the total SGenius software coding by yours truly. This modified Levenberg-Marquardt optimization corresponds to a Newton algorithm with an adapted damping parameter regarding the definition domains of the optimized parameters. Currently, S-Genius is technically ready for scientific collaboration, python-powered, multi-platform (windows/linux/macOS), multi-core, ready for 2D- (infinite features along the direction perpendicular to the incident plane), conical, and 3D-features computation, compatible with all kinds of input data from any possible ellipsometers (angle or wavelength resolved) or reflectometers, and widely used in our laboratory for resist trimming studies, etching features characterization (such as complex stack) or nano-imprint lithography measurements for instance. The work about kriging solver, neural network solver and material refractive indices determination is done (or about to) by other LTM members and about to be integrated on S-Genius platform.

Intruder signature analysis from a phase-sensitive distributed fiber-optic perimeter sensor

NASA Astrophysics Data System (ADS)

Madsen, C. K.; Bae, T.; Snider, T.

2007-09-01

Using a phase-sensitive optical time-domain reflectometer developed at Texas A&M University, this paper reports on recent advances in intruder detection and classificatoin for long perimeters or borders. The system uses light pulses from a narrow linewidth CW laser with low frequency drift to interrogate an optical fiber. The backscattered light is detected, and real-time processing of the received signal is performed. Signatures from single and multiple humans on foot, nearby vehicle traffic on a road, construction-like vehicle activity, and animals have been obtained. Individual footsteps are clearly identified and the cadence readily observed. Time-frequency plots are used to compare the signatures. The detected signal contains information regarding the weight of the intruder as well. An adult weighing around 60kg may produce several π-radian shifts in the optical phase, which is detected by the system. While distances up to 20km have been monitored in previous remote field tests, we report measurements on a local test site with a total fiber length of 12km. A 3-mm diameter fiber cable is buried at a depth of 20-46 cm over a distance of 44m, with a 2km spool of fiber attached prior to the buried fiber and a 10km fiber spool connected in series after the buried section. Recent advances in data acquisition and signal processing allow us to avoid false alarms due to drifts in the laser center frequency and greatly improve the probability of detection. With these advancements, this technology is prime for low-cost perimeter monitoring of high-value and high-security installations such as nuclear power plants and military bases as well as national borders.

Distributed fiber optic intrusion sensor system for monitoring long perimeters

NASA Astrophysics Data System (ADS)

Juarez, Juan C.; Taylor, Henry F.

2005-05-01

The use of an optical fiber as a distributed sensor for detecting and locating intruders over long perimeters (>10 km) is described. Phase changes resulting from either the pressure of the intruder on the ground immediately above the buried fiber or from seismic disturbances in the vicinity are sensed by a phase-sensitive optical time-domain reflectometer (Φ-OTDR). Light pulses from a cw laser operating in a single longitudinal mode and with low (MHz/min range) frequency drift are injected into one end of the single mode fiber, and the backscattered light is monitored with a photodetector. In laboratory tests with 12 km of fiber on reels, the effects of localized phase perturbations induced by a piezoelectric fiber stretcher on Φ-OTDR traces were characterized. In field tests in which the sensing element is a single mode fiber in a 3-mm diameter cable buried in a 20-46 cm deep, 10 cm wide trench in clay soil, detection of intruders on foot up to 4.6 m from the cable line was achieved. In desert terrain field tests in which the sensing fiber is in a 4.5-mm diameter cable buried in a 30 cm deep, 75 cm wide trench filled with loose sand, high sensitivity and consistent detection of intruders on foot and of vehicles traveling down a road near the cable line was realized over a cable length of 8.5 km and a total fiber path of 19 km. Based on these results, this technology may be regarded as a candidate for providing low-cost perimeter security for nuclear power plants, electrical power distribution centers, storage facilities for fuel and volatile chemicals, communication hubs, airports, government offices, military bases, embassies, and national borders.

A conserved glutamine plays a central role in LOV domain signal transmission and duration

PubMed Central

Nash, Abigail I.; Ko, Wen-Huang; Harper, Shannon M.; Gardner, Kevin H.

2009-01-01

Light is a key stimulus for plant biological functions, several of which are controlled by light-activated kinases known as phototropins, a group of kinases that contain two light-sensing domains (LOV, Light-Oxygen-Voltage domains) and a C-terminal serine/threonine kinase domain. The second sensory domain, LOV2, plays a key role in regulating kinase enzymatic activity via the photochemical formation of a covalent adduct between a LOV2 cysteine residue and an internally-bound flavin mononucleotide (FMN) chromophore. Subsequent conformational changes in LOV2 lead to the unfolding of a peripheral Jα helix, and ultimately, phototropin kinase activation. To date, the mechanism coupling bond formation and helix dissociation has remained unclear. Previous studies found that a conserved glutamine residue (Q513 in the Avena sativa phototropin 1 LOV2 (AsLOV2) domain) switches its hydrogen-bonding pattern with FMN upon light stimulation. Located in the immediate vicinity of the FMN binding site, this Gln residue is provided by the Iβ strand that interacts with the Jα helix, suggesting a route for signal propagation from the core of the LOV domain to its peripheral Jα helix. To test whether Q513 plays a key role in tuning the photochemical and transduction properties of AsLOV2, we designed two point mutations, Q513L and Q513N, and monitored the effects on the chromophore and protein using a combination of UV-visible absorbance and circular dichroism spectroscopy, limited proteolysis, and solution NMR. The results show that these mutations significantly dampen the changes between the dark and lit state AsLOV2 structures, leaving the protein in a pseudo-dark state (Q513L) or a pseudo-lit state (Q513N) conformation. Further, both mutations changed the photochemical properties of this receptor, particularly the lifetime of the photoexcited signaling states. Together, these data establish that this residue plays a central role in both spectral tuning and signal propagation from the core of the LOV domain through the Iβ strand to the peripheral Jα helix. PMID:19063612

Formation and stability of synaptic receptor domains.

PubMed

Haselwandter, Christoph A; Calamai, Martino; Kardar, Mehran; Triller, Antoine; da Silveira, Rava Azeredo

2011-06-10

Neurotransmitter receptor molecules, concentrated in postsynaptic domains along with scaffold and a number of other molecules, are key regulators of signal transmission across synapses. Combining experiment and theory, we develop a quantitative description of synaptic receptor domains in terms of a reaction-diffusion model. We show that interactions between only receptors and scaffolds, together with the rapid diffusion of receptors on the cell membrane, are sufficient for the formation and stable characteristic size of synaptic receptor domains. Our work reconciles long-term stability of synaptic receptor domains with rapid turnover and diffusion of individual receptors, and suggests novel mechanisms for a form of short-term, postsynaptic plasticity.

Evolution and Classification of Myosins, a Paneukaryotic Whole-Genome Approach

PubMed Central

Sebé-Pedrós, Arnau; Grau-Bové, Xavier; Richards, Thomas A.; Ruiz-Trillo, Iñaki

2014-01-01

Myosins are key components of the eukaryotic cytoskeleton, providing motility for a broad diversity of cargoes. Therefore, understanding the origin and evolutionary history of myosin classes is crucial to address the evolution of eukaryote cell biology. Here, we revise the classification of myosins using an updated taxon sampling that includes newly or recently sequenced genomes and transcriptomes from key taxa. We performed a survey of eukaryotic genomes and phylogenetic analyses of the myosin gene family, reconstructing the myosin toolkit at different key nodes in the eukaryotic tree of life. We also identified the phylogenetic distribution of myosin diversity in terms of number of genes, associated protein domains and number of classes in each taxa. Our analyses show that new classes (i.e., paralogs) and domain architectures were continuously generated throughout eukaryote evolution, with a significant expansion of myosin abundance and domain architectural diversity at the stem of Holozoa, predating the origin of animal multicellularity. Indeed, single-celled holozoans have the most complex myosin complement among eukaryotes, with paralogs of most myosins previously considered animal specific. We recover a dynamic evolutionary history, with several lineage-specific expansions (e.g., the myosin III-like gene family diversification in choanoflagellates), convergence in protein domain architectures (e.g., fungal and animal chitin synthase myosins), and important secondary losses. Overall, our evolutionary scheme demonstrates that the ancestral eukaryote likely had a complex myosin repertoire that included six genes with different protein domain architectures. Finally, we provide an integrative and robust classification, useful for future genomic and functional studies on this crucial eukaryotic gene family. PMID:24443438

Optical image encryption by random shifting in fractional Fourier domains

NASA Astrophysics Data System (ADS)

Hennelly, B.; Sheridan, J. T.

2003-02-01

A number of methods have recently been proposed in the literature for the encryption of two-dimensional information by use of optical systems based on the fractional Fourier transform. Typically, these methods require random phase screen keys for decrypting the data, which must be stored at the receiver and must be carefully aligned with the received encrypted data. A new technique based on a random shifting, or jigsaw, algorithm is proposed. This method does not require the use of phase keys. The image is encrypted by juxtaposition of sections of the image in fractional Fourier domains. The new method has been compared with existing methods and shows comparable or superior robustness to blind decryption. Optical implementation is discussed, and the sensitivity of the various encryption keys to blind decryption is examined.

Novel image encryption algorithm based on multiple-parameter discrete fractional random transform

NASA Astrophysics Data System (ADS)

Zhou, Nanrun; Dong, Taiji; Wu, Jianhua

2010-08-01

A new method of digital image encryption is presented by utilizing a new multiple-parameter discrete fractional random transform. Image encryption and decryption are performed based on the index additivity and multiple parameters of the multiple-parameter fractional random transform. The plaintext and ciphertext are respectively in the spatial domain and in the fractional domain determined by the encryption keys. The proposed algorithm can resist statistic analyses effectively. The computer simulation results show that the proposed encryption algorithm is sensitive to the multiple keys, and that it has considerable robustness, noise immunity and security.

Semantics driven approach for knowledge acquisition from EMRs.

PubMed

Perera, Sujan; Henson, Cory; Thirunarayan, Krishnaprasad; Sheth, Amit; Nair, Suhas

2014-03-01

Semantic computing technologies have matured to be applicable to many critical domains such as national security, life sciences, and health care. However, the key to their success is the availability of a rich domain knowledge base. The creation and refinement of domain knowledge bases pose difficult challenges. The existing knowledge bases in the health care domain are rich in taxonomic relationships, but they lack nontaxonomic (domain) relationships. In this paper, we describe a semiautomatic technique for enriching existing domain knowledge bases with causal relationships gleaned from Electronic Medical Records (EMR) data. We determine missing causal relationships between domain concepts by validating domain knowledge against EMR data sources and leveraging semantic-based techniques to derive plausible relationships that can rectify knowledge gaps. Our evaluation demonstrates that semantic techniques can be employed to improve the efficiency of knowledge acquisition.

The Domain-Specificity of Creativity: Insights from New Phenomenology

ERIC Educational Resources Information Center

Julmi, Christian; Scherm, Ewald

2015-01-01

The question of the domain-specificity of creativity represents one of the key questions in creativity research. This article contributes to the discussion by applying insights from "new phenomenology," which is a phenomenological movement from Germany initiated by philosopher Hermann Schmitz. The findings of new phenomenology suggest…

Expert Concept Mapping Study on Mobile Learning

ERIC Educational Resources Information Center

Borner, Dirk; Glahn, Christian; Stoyanov, Slavi; Kalz, Marco; Specht, Marcus

2010-01-01

Purpose: The present paper introduces concept mapping as a structured participative conceptualization approach to identify clusters of ideas and opinions generated by experts within the domain of mobile learning. Utilizing this approach, the paper aims to contribute to a definition of key domain characteristics by identifying the main educational…

Missing links between histones and RNA Pol II arising from SAND?

USDA-ARS?s Scientific Manuscript database

Eukaryotic SAND domain-containing proteins bind DNA and are implicated in direct target gene activation and chromatin-mediated gene regulation. We summarize our recent results demonstrating that the Arabidopsis SAND domain protein ULTRAPETALA1 (ULT1) plays a key role in counteracting target gene rep...

Positioning Mathematics Education Researchers to Influence Storylines

ERIC Educational Resources Information Center

Herbel-Eisenmann, Beth; Sinclair, Nathalie; Chval, Kathryn B.; Clements, Douglas H.; Civil, Marta; Pape, Stephen J.; Stephan, Michelle; Wanko, Jeffrey J.; Wilkerson, Trena L.

2016-01-01

The NCTM Research Committee identifies key influences on mathematics education that are largely outside the domain of the academic world in which most mathematics education researchers live. The groups that are identified--including the media, companies and foundations, and other academic domains--affect the public's perception of mathematics and…

Learning Portals: Analyzing Threshold Concept Theory for LIS Education

ERIC Educational Resources Information Center

Tucker, Virginia M.; Weedman, Judith; Bruce, Christine S.; Edwards, Sylvia L.

2014-01-01

This paper explores the theoretical framework of threshold concepts and its potential for LIS education. Threshold concepts are key ideas, often troublesome and counterintuitive, that are critical to profound understanding of a domain. Once understood, they allow mastery of significant aspects of the domain, opening up new, previously inaccessible…

Application of the Haar Wavelet to the Analysis of Plasma and Atmospheric Fluctuations

NASA Astrophysics Data System (ADS)

Maslov, S. A.; Kharchevsky, A. A.; Smirnov, V. A.

2017-12-01

The parameters of turbulence measured by means of a Doppler reflectometer at the plasma periphery in an L-2M stellarator and in atmospheric vortices (typhoons and tornadoes) are investigated using the wavelet methods with involvement of the Haar function. The periods of time taken for the transition (a bound of parameters) to occur in the L-2M stellarator plasma and in atmospheric processes are estimated. It is shown that high-and low-frequency oscillations of certain parameters, in particular, pressure, that occur in atmospheric vortices decay or increase at different moments of time, whereas the density fluctuation amplitudes that occur in plasma at different frequencies vary in a synchronous manner.

A millimeter-wave reflectometer for whole-body hydration sensing

NASA Astrophysics Data System (ADS)

Zhang, W.-D.; Brown, E. R.

2016-05-01

This paper demonstrates a non-invasive method to determine the hydration level of human skin by measuring the reflectance of W-band (75-110 GHz) and Ka-band (26-40 GHz) radiation. Ka-band provides higher hydration accuracy (<1%) and greater depth of penetration (> 1 mm), thereby allowing access to the important dermis layer of skin. W-band provides less depth of penetration but finer spatial resolution (~2 mm). Both the hydration sensing concept and experimental results are presented here. The goal is to make a human hydration sensor that is 1% accurate or better, operable by mechanically scanning, and fast enough to measure large areas of the human body in seconds.

Polarization effects on hard target calibration of lidar systems

NASA Technical Reports Server (NTRS)

Kavaya, Michael J.

1987-01-01

The theory of hard target calibration of lidar backscatter data, including laboratory measurements of the pertinent target reflectance parameters, is extended to include the effects of polarization of the transmitted and received laser radiation. The bidirectional reflectance-distribution function model of reflectance is expanded to a 4 x 4 matrix allowing Mueller matrix and Stokes vector calculus to be employed. Target reflectance parameters for calibration of lidar backscatter data are derived for various lidar system polarization configurations from integrating sphere and monostatic reflectometer measurements. It is found that correct modeling of polarization effects is mandatory for accurate calibration of hard target reflectance parameters and, therefore, for accurate calibration of lidar backscatter data.

Far-infrared /FIR/ optical black bidirectional reflectance distribution function /BRDF/

NASA Technical Reports Server (NTRS)

Smith, S. M.

1981-01-01

A nonspecular reflectometer and its operation at far-infrared wavelengths are described. Large differences in nonspecular reflectance were found to exist between different optically black coatings. Normal incidence bidirectional reflectance distribution function /BRDF) measurements at wavelengths between 12 and 316 microns of three black coatings show that their mean BRDFs increase with wavelength. The specularity of two of these coatings also showed a strong wavelength dependence, while the specularity of one coating seemed independent of wavelength. The BRDF of one coating depended on the angle of incidence at 12 and 38 microns, but not at 316 microns. Beyond 200 microns, it was found necessary to correct the measurements for the beam spread of the instrument.

Update to permeable pavement research at the Edison ...

EPA Pesticide Factsheets

Abstract: The EPA’s Urban Watershed Management Branch (UWMB) has been monitoring the permeable pavement demonstration site at the Edison Environmental Center, NJ since 2010. This site has three different types of permeable pavement including: interlocking concrete permeable pavers; porous concrete; and permeable asphalt. The parking lot is instrumented with water content reflectometers and thermistors for continuous monitoring and has four lined sections for each surface to capture permeable pavement infiltrate for water quality analyses.Previous technical releases concerning the demonstration site focused on monitoring techniques, observed chloride and nutrient concentrations, and infiltration and evaporation rates. Thispresentation summarizes past findings and addresses current water quality efforts. This presentation summarizes past findings and addresses current water quality efforts.

Crystal structure of a shark single-domain antibody V region in complex with lysozyme.

PubMed

Stanfield, Robyn L; Dooley, Helen; Flajnik, Martin F; Wilson, Ian A

2004-09-17

Cartilaginous fish are the phylogenetically oldest living organisms known to possess components of the vertebrate adaptive immune system. Key to their immune response are heavy-chain, homodimeric immunoglobulins called new antigen receptors (IgNARs), in which the variable (V) domains recognize antigens with only a single immunoglobulin domain, akin to camelid heavy-chain V domains. The 1.45 angstrom resolution crystal structure of the type I IgNAR V domain in complex with hen egg-white lysozyme (HEL) reveals a minimal antigen-binding domain that contains only two of the three conventional complementarity-determining regions but still binds HEL with nanomolar affinity by means of a binding interface comparable in size to conventional antibodies.

Secret shared multiple-image encryption based on row scanning compressive ghost imaging and phase retrieval in the Fresnel domain

NASA Astrophysics Data System (ADS)

Li, Xianye; Meng, Xiangfeng; Wang, Yurong; Yang, Xiulun; Yin, Yongkai; Peng, Xiang; He, Wenqi; Dong, Guoyan; Chen, Hongyi

2017-09-01

A multiple-image encryption method is proposed that is based on row scanning compressive ghost imaging, (t, n) threshold secret sharing, and phase retrieval in the Fresnel domain. In the encryption process, after wavelet transform and Arnold transform of the target image, the ciphertext matrix can be first detected using a bucket detector. Based on a (t, n) threshold secret sharing algorithm, the measurement key used in the row scanning compressive ghost imaging can be decomposed and shared into two pairs of sub-keys, which are then reconstructed using two phase-only mask (POM) keys with fixed pixel values, placed in the input plane and transform plane 2 of the phase retrieval scheme, respectively; and the other POM key in the transform plane 1 can be generated and updated by the iterative encoding of each plaintext image. In each iteration, the target image acts as the input amplitude constraint in the input plane. During decryption, each plaintext image possessing all the correct keys can be successfully decrypted by measurement key regeneration, compression algorithm reconstruction, inverse wavelet transformation, and Fresnel transformation. Theoretical analysis and numerical simulations both verify the feasibility of the proposed method.

From Domain Specific Languages to DEVS Components: Application to Cognitive M&S

DTIC Science & Technology

2011-04-01

AND SUBTITLE From Domain Specific Languages to DEVS Components: Application to Cognitive M&S 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ...that is devoid of any DEVS and programming language constructs (Figure 4). The key idea being domain specialists need not delve in the DEVS world to...DSL. DSLs can be created using many available tools and technologies such as: Generic Modeling Environment (GME) [23], Xtext, Ruby, Scala and many

Behaviors and Knowledge of HealthCorps New York City High School Students: Nutrition, Mental Health and Physical Activity

PubMed Central

Moonseong, Heo; Erica, Irvin; Natania, Ostrovsky; Carmen, Isasi; Shawn, Hayes; Judith, Wylie-Rosett

2015-01-01

BACKGROUND HealthCorps provides school wellness programming using curricula to promote changes in nutrition, mental health and physical activity behaviors. The research objective was to evaluate effects of implementing its curricula on nutrition, mental health and physical activity knowledge and behavior. METHODS Pre- and post-survey data were collected (N = 2255) during the 2012-13 academic year from 14 New York City public high schools. An 18-item knowledge questionnaire addressed 3 domains; 26 behavioral items were analyzed by factor analysis to identify 6 behavior domains, breakfast being a seventh one-item domain. We examined the effects stratified by sex, applying mixed-effects models to take into account clustering effects of schools and participants adjusted for age. RESULTS The HealthCorps program significantly increased all 3 knowledge domains (p < .05), and significantly changed several key behavioral domains. Boys significantly increased fruits/vegetables intake (p = .03). Girls increased acceptance of new fruits/vegetables (p = .03) and breakfast consumption (p = .04), and decreased sugar-sweetened beverages and energy dense food intake (p = .03). The associations between knowledge and behavior were stronger in boys than girls. CONCLUSION The HealthCorps program significantly increased participants’ knowledge on nutrition, mental health and physical activity. It also improved several key behavioral domains, which are targets of the 2010 Dietary Guidelines to address obesity in youth. PMID:26762819

Behaviors and Knowledge of HealthCorps New York City High School Students: Nutrition, Mental Health, and Physical Activity.

PubMed

Heo, Moonseong; Irvin, Erica; Ostrovsky, Natania; Isasi, Carmen; Blank, Arthur E; Lounsbury, David W; Fredericks, Lynn; Yom, Tiana; Ginsberg, Mindy; Hayes, Shawn; Wylie-Rosett, Judith

2016-02-01

HealthCorps provides school wellness programming using curricula to promote changes in nutrition, mental health, and physical activity behaviors. The research objective was to evaluate effects of implementing its curricula on nutrition, mental health, and physical activity knowledge and behavior. Pre- and postsurvey data were collected (N = 2255) during the 2012-2013 academic year from 14 New York City public high schools. An 18-item knowledge questionnaire addressed 3 domains; 26 behavioral items were analyzed by factor analysis to identify 6 behavior domains, breakfast being a seventh 1-item domain. We examined the effects stratified by sex, applying mixed-effects models to take into account clustering effects of schools and participants adjusted for age. The HealthCorps program significantly increased all 3 knowledge domains (p < .05), and significantly changed several key behavioral domains. Boys significantly increased fruits/vegetables intake (p = .03). Girls increased acceptance of new fruits/vegetables (p = .03) and breakfast consumption (p = .04), and decreased sugar-sweetened beverages and energy dense food intake (p = .03). The associations between knowledge and behavior were stronger in boys than girls. The HealthCorps program significantly increased participants' knowledge on nutrition, mental health, and physical activity. It also improved several key behavioral domains, which are targets of the 2010 Dietary Guidelines to address obesity in youth. © 2016, American School Health Association.

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

NASA Astrophysics Data System (ADS)

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; Yang, Jun; Han, Gye Won; Zhao, Suwen; Ishchenko, Andrii; Ye, Lintao; Lin, Xi; Ding, Kang; Dharmarajan, Venkatasubramanian; Griffin, Patrick R.; Gati, Cornelius; Nelson, Garrett; Hunter, Mark S.; Hanson, Michael A.; Cherezov, Vadim; Stevens, Raymond C.; Tan, Wenfu; Tao, Houchao; Xu, Fei

2017-05-01

The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.

Comparing Personal Characteristic Factors of Imagination between Expert and Novice Designers within Different Product Design Stages

ERIC Educational Resources Information Center

Huang, Yinghsiu; Li, Jianyou

2015-01-01

Imagination plays a key role in various domains in helping to create innovative ideas, drawings, poems, movies, products, etc. In product design domain, the personal characteristics of imagination are crucial abilities for conceiving novel ideas during design processes. This study focuses on personal characteristic differences and similarities…

Image encryption with chaotic map and Arnold transform in the gyrator transform domains

NASA Astrophysics Data System (ADS)

Sang, Jun; Luo, Hongling; Zhao, Jun; Alam, Mohammad S.; Cai, Bin

2017-05-01

An image encryption method combing chaotic map and Arnold transform in the gyrator transform domains was proposed. Firstly, the original secret image is XOR-ed with a random binary sequence generated by a logistic map. Then, the gyrator transform is performed. Finally, the amplitude and phase of the gyrator transform are permutated by Arnold transform. The decryption procedure is the inverse operation of encryption. The secret keys used in the proposed method include the control parameter and the initial value of the logistic map, the rotation angle of the gyrator transform, and the transform number of the Arnold transform. Therefore, the key space is large, while the key data volume is small. The numerical simulation was conducted to demonstrate the effectiveness of the proposed method and the security analysis was performed in terms of the histogram of the encrypted image, the sensitiveness to the secret keys, decryption upon ciphertext loss, and resistance to the chosen-plaintext attack.

Emerging roles of post-translational modifications in signal transduction and angiogenesis.

PubMed

Rahimi, Nader; Costello, Catherine E

2015-01-01

The vascular endothelial growth factor receptor-2 (VEGFR-2) belongs to the family of receptor tyrosine kinases and is a key player in vasculogenesis and pathological angiogenesis. An emerging picture of PTMs of VEGFR-2 suggests that they play central roles in generating a highly dynamic and complex signaling system that regulates key angiogenic responses ranging from endothelial cell differentiation, proliferation, migration to permeability. Recent MS analysis of VEGFR-2 uncovered previously unrecognized PTMs on VEGFR-2 with a distinct function. The ligand binding extracellular domain of VEGFR-2 is composed of seven immunoglobulin-like domains highly decorated with N-glycosylation, while its cytoplasmic domain is subject to multiple PTMs including Tyr, Ser/Thr phosphorylation, Arg and Lys methylation, acetylation and ubiquitination. Here we review the PTMs on VEGFR-2, their importance in angiogenic signaling relays and possible novel therapeutic potentials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-Domain Transfer Learning for Early Diagnosis of Alzheimer's Disease.

PubMed

Cheng, Bo; Liu, Mingxia; Shen, Dinggang; Li, Zuoyong; Zhang, Daoqiang

2017-04-01

Recently, transfer learning has been successfully applied in early diagnosis of Alzheimer's Disease (AD) based on multi-domain data. However, most of existing methods only use data from a single auxiliary domain, and thus cannot utilize the intrinsic useful correlation information from multiple domains. Accordingly, in this paper, we consider the joint learning of tasks in multi-auxiliary domains and the target domain, and propose a novel Multi-Domain Transfer Learning (MDTL) framework for early diagnosis of AD. Specifically, the proposed MDTL framework consists of two key components: 1) a multi-domain transfer feature selection (MDTFS) model that selects the most informative feature subset from multi-domain data, and 2) a multi-domain transfer classification (MDTC) model that can identify disease status for early AD detection. We evaluate our method on 807 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database using baseline magnetic resonance imaging (MRI) data. The experimental results show that the proposed MDTL method can effectively utilize multi-auxiliary domain data for improving the learning performance in the target domain, compared with several state-of-the-art methods.

Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design.

PubMed

Corradi, Hazel R; Schwager, Sylva L U; Nchinda, Aloysius T; Sturrock, Edward D; Acharya, K Ravi

2006-03-31

Human somatic angiotensin I-converting enzyme (sACE) is a key regulator of blood pressure and an important drug target for combating cardiovascular and renal disease. sACE comprises two homologous metallopeptidase domains, N and C, joined by an inter-domain linker. Both domains are capable of cleaving the two hemoregulatory peptides angiotensin I and bradykinin, but differ in their affinities for a range of other substrates and inhibitors. Previously we determined the structure of testis ACE (C domain); here we present the crystal structure of the N domain of sACE (both in the presence and absence of the antihypertensive drug lisinopril) in order to aid the understanding of how these two domains differ in specificity and function. In addition, the structure of most of the inter-domain linker allows us to propose relative domain positions for sACE that may contribute to the domain cooperativity. The structure now provides a platform for the design of "domain-specific" second-generation ACE inhibitors.

Testing key predictions of the associative account of mirror neurons in humans using multivariate pattern analysis.

PubMed

Oosterhof, Nikolaas N; Wiggett, Alison J; Cross, Emily S

2014-04-01

Cook et al. overstate the evidence supporting their associative account of mirror neurons in humans: most studies do not address a key property, action-specificity that generalizes across the visual and motor domains. Multivariate pattern analysis (MVPA) of neuroimaging data can address this concern, and we illustrate how MVPA can be used to test key predictions of their account.

Measuring Mars' Atmospheric Neutral Density from 160 to 220km with the MGS Electron Reflectometer

NASA Astrophysics Data System (ADS)

Lillis, R.; Engel, J.; Mitchell, D.; Brain, D.; Lin, R.; Bougher, S.; Acuna, M.

2005-08-01

The Magnetometer/Electron Reflectometer (MAG/ER) experiment aboard Mars Global Surveyor (MGS) samples the local electron population's distribution in energy and pitch angle (angle between electron velocity and local magnetic field direction) at the mapping orbit altitude of ˜400km. We develop a single-particle model of the electrons' interaction with the neutral atmosphere and motion along open field-lines connecting the solar wind to remnant crustal magnetization. Electron reflection from magnetic gradients and absorption due to inelastic collisons with atmospheric neutrals results in characteristic pitch angle (PA) distributions for open field lines. By assuming the validity of spherical harmonic expansions (Cain et al, 2003) in the strongest field regions of Mars (such as Terra Sirenum), we trace the electron paths and fit these PA distributions to our model to constrain the scale height and density of the neutral atmosphere in the region of greatest absorption, 160-220km. We analyse almost 3 martian years of MGS mapping Orbit Data and present the first measurements of Mars' neutral density above 180km. Although the uncertainties in single measurements are quite large, averaging over many measurements over a period of weeks allows us to see long-term trends. Major results are: 1) a mean density of 0.03 kg/km3 at 160km with a month-averaged variation of ˜40%, 2) a very strong annual seasonal variation, confirmed by periodogram and least-squares fit and 3) increasing seasonal density variability with distance from the equator. We see broad general agreement with predictions from Mars Thermosphere Global Circulation Model (MTGCM) simulations [Bougher et al, 2004] and with inferred densities from MGS Doppler tracking data [Tracadas et al, 2001]. Our results will help to constrain the upper boundaries of GCMs and assist orbital decay calculations for low-orbiting spacecraft, such as the 2005 Mars Reconnaissance Orbiter. We thank the NASA Jet Propulsion Laboratory for funding assistance for this research.

Evaluation of quick tests for phosphorus determination in dairy manures.

PubMed

Lugo-Ospina, A; Dao, Thanh H; Van Kessel, J A; Reeves, J B

2005-05-01

Nutrients in animal manure are valuable inputs in agronomic crop production. Rapid and timely information about manure nutrient content are needed to minimize the risks of phosphorus (P) over-application and losses of dissolved P (DP) in runoff from fields treated with manure. We evaluated the suitability of a commercial hand-held reflectometer, a hydrometer, and an electrical conductivity (EC) meter for determining DP and total P (TP) in dairy manures. Bulk samples (n = 107) collected from farms across CT, MD, NY, PA, and VA were highly variable in total solids (TS) concentration, ranging from 11 to 213gL(-1), in suspensions' pH (6.3-9.2), and EC (6.2-53.3 dS m(-1)). Manure DP concentrations measured using the RQFlex reflectometer (RQFlex-DP(s)) were related to molybdate-reactive P (MRP(s)) concentrations as follows: RQFlex-DP(s) = 0.471 x MRP(s) + 1102 (r2 = 0.29). Inclusion of pH and squared-pH terms improved the prediction of manure DP from RQFlex results (r2 = 0.66). Excluding five outlier samples that had pH < or = 6.9 the coefficient of determination (r2) for the MRP(s) and RQFlex-DP(s) relationship was 0.83 for 95% of the samples. Manure TS were related to hydrometer specific gravity readings (r2 = 0.53) that were in turn related to TP (r2 = 0.34), but not to either RQFlex-DP or MRP. Relationships between suspensions' EC and DP or TP were non-significant. Therefore, the RQFlex method is the only viable option for on-site quick estimates of DP that can be made more robust when complemented with TS and pH measurements. The DP quick test can provide near real-time information on soluble manure nutrient content across a wide range of handling and storage conditions on dairy farms and quick estimates of potential soluble P losses in runoff following land applications of manure.

Effectiveness of Cool Roof Coatings with Ceramic Particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brehob, Ellen G; Desjarlais, Andre Omer; Atchley, Jerald Allen

2011-01-01

Liquid applied coatings promoted as cool roof coatings, including several with ceramic particles, were tested at Oak Ridge National Laboratory (ORNL), Oak Ridge, Tenn., for the purpose of quantifying their thermal performances. Solar reflectance measurements were made for new samples and aged samples using a portable reflectometer (ASTM C1549, Standard Test Method for Determination of Solar Reflectance Near Ambient Temperature Using a Portable Solar Reflectometer) and for new samples using the integrating spheres method (ASTM E903, Standard Test Method for Solar Absorptance, Reflectance, and Transmittance of Materials Using Integrating Spheres). Thermal emittance was measured for the new samples using amore » portable emissometer (ASTM C1371, Standard Test Method for Determination of Emittance of Materials Near Room 1 Proceedings of the 2011 International Roofing Symposium Temperature Using Portable Emissometers). Thermal conductivity of the coatings was measured using a FOX 304 heat flow meter (ASTM C518, Standard Test Method for Steady-State Thermal Transmission Properties by Means of the Heat Flow Meter Apparatus). The surface properties of the cool roof coatings had higher solar reflectance than the reference black and white material, but there were no significant differences among coatings with and without ceramics. The coatings were applied to EPDM (ethylene propylene diene monomer) membranes and installed on the Roof Thermal Research Apparatus (RTRA), an instrumented facility at ORNL for testing roofs. Roof temperatures and heat flux through the roof were obtained for a year of exposure in east Tennessee. The field tests showed significant reduction in cooling required compared with the black reference roof (~80 percent) and a modest reduction in cooling compared with the white reference roof (~33 percent). The coating material with the highest solar reflectivity (no ceramic particles) demonstrated the best overall thermal performance (combination of reducing the cooling load cost and not incurring a large heating penalty cost) and suggests solar reflectivity is the significant characteristic for selecting cool roof coatings.« less

Proline Substitutions and Threonine Pseudophosphorylation of the SH3 Ligand of 18.5-kDa Myelin Basic Protein Decrease Its Affinity for the Fyn-SH3 Domain and Alter Process Development and Protein Localization in Oligodendrocytes

PubMed Central

Smith, Graham S.T.; De Avila, Miguel; Paez, Pablo M.; Spreuer, Vilma; Wills, Melanie K.B.; Jones, Nina; Boggs, Joan M.; Harauz, George

2012-01-01

The developmentally regulated myelin basic proteins (MBPs), which arise from the golli (gene of oligodendrocyte lineage) complex, are highly positively charged, intrinsically disordered, multifunctional proteins having several alternatively spliced isoforms and posttranslational modifications, and they play key roles in myelin compaction. The classic 18.5-kDa MBP isoform has a proline-rich region comprising amino acids 92–99 (murine sequence –T92PRTPPPS99–) that contains a minimal SH3 ligand domain. We have previously shown that 18.5-kDa MBP binds to several SH3 domains, including that of Fyn, a member of the Src family of tyrosine kinases involved in a number of signaling pathways during CNS development. To determine the physiological role of this binding as well as the role of phosphorylation of Thr92 and Thr95, in the current study we have produced several MBP variants specifically targeting phosphorylation sites and key structural regions of MBP’s SH3 ligand domain. Using isothermal titration calorimetry, we have demonstrated that, compared with the wild-type protein, these variants have lower affinity for the SH3 domain of Fyn. Moreover, overexpression of N-terminal-tagged GFP versions in immortalized oligodendroglial N19 and N20.1 cell cultures results in aberrant elongation of membrane processes and increased branching complexity and inhibits the ability of MBP to decrease Ca2+ influx. Phosphorylation of Thr92 can also cause MBP to traffic to the nucleus, where it may participate in additional protein–protein interactions. Coexpression of MBP with a constitutively active form of Fyn kinase resulted in membrane process elaboration, a phenomenon that was abolished by point amino acid substitutions in MBP’s SH3 ligand domain. These results suggest that MBP’s SH3 ligand domain plays a key role in intracellular protein interactions in vivo and may be required for proper membrane elaboration of developing oligodendrocytes and, further, that phosphorylation of Thr92 and Thr95 can regulate this function. PMID:21887699

Proline substitutions and threonine pseudophosphorylation of the SH3 ligand of 18.5-kDa myelin basic protein decrease its affinity for the Fyn-SH3 domain and alter process development and protein localization in oligodendrocytes.

PubMed

Smith, Graham S T; De Avila, Miguel; Paez, Pablo M; Spreuer, Vilma; Wills, Melanie K B; Jones, Nina; Boggs, Joan M; Harauz, George

2012-01-01

The developmentally regulated myelin basic proteins (MBPs), which arise from the golli (gene of oligodendrocyte lineage) complex, are highly positively charged, intrinsically disordered, multifunctional proteins having several alternatively spliced isoforms and posttranslational modifications, and they play key roles in myelin compaction. The classic 18.5-kDa MBP isoform has a proline-rich region comprising amino acids 92-99 (murine sequence -T(92)PRTPPPS(99)-) that contains a minimal SH3 ligand domain. We have previously shown that 18.5-kDa MBP binds to several SH3 domains, including that of Fyn, a member of the Src family of tyrosine kinases involved in a number of signaling pathways during CNS development. To determine the physiological role of this binding as well as the role of phosphorylation of Thr92 and Thr95, in the current study we have produced several MBP variants specifically targeting phosphorylation sites and key structural regions of MBP's SH3 ligand domain. Using isothermal titration calorimetry, we have demonstrated that, compared with the wild-type protein, these variants have lower affinity for the SH3 domain of Fyn. Moreover, overexpression of N-terminal-tagged GFP versions in immortalized oligodendroglial N19 and N20.1 cell cultures results in aberrant elongation of membrane processes and increased branching complexity and inhibits the ability of MBP to decrease Ca(2+) influx. Phosphorylation of Thr92 can also cause MBP to traffic to the nucleus, where it may participate in additional protein-protein interactions. Coexpression of MBP with a constitutively active form of Fyn kinase resulted in membrane process elaboration, a phenomenon that was abolished by point amino acid substitutions in MBP's SH3 ligand domain. These results suggest that MBP's SH3 ligand domain plays a key role in intracellular protein interactions in vivo and may be required for proper membrane elaboration of developing oligodendrocytes and, further, that phosphorylation of Thr92 and Thr95 can regulate this function. Copyright © 2011 Wiley Periodicals, Inc.

Conceptualizing Community Mobilization for HIV Prevention: Implications for HIV Prevention Programming in the African Context

PubMed Central

Lippman, Sheri A.; Maman, Suzanne; MacPhail, Catherine; Twine, Rhian; Peacock, Dean; Kahn, Kathleen; Pettifor, Audrey

2013-01-01

Introduction Community mobilizing strategies are essential to health promotion and uptake of HIV prevention. However, there has been little conceptual work conducted to establish the core components of community mobilization, which are needed to guide HIV prevention programming and evaluation. Objectives We aimed to identify the key domains of community mobilization (CM) essential to change health outcomes or behaviors, and to determine whether these hypothesized CM domains were relevant to a rural South African setting. Method We studied social movements and community capacity, empowerment and development literatures, assessing common elements needed to operationalize HIV programs at a community level. After synthesizing these elements into six essential CM domains, we explored the salience of these CM domains qualitatively, through analysis of 10 key informant in-depth-interviews and seven focus groups in three villages in Bushbuckridge. Results CM domains include: 1) shared concerns, 2) critical consciousness, 3) organizational structures/networks, 4) leadership (individual and/or institutional), 5) collective activities/actions, and 6) social cohesion. Qualitative data indicated that the proposed domains tapped into theoretically consistent constructs comprising aspects of CM processes. Some domains, extracted from largely Western theory, required little adaptation for the South African context; others translated less effortlessly. For example, critical consciousness to collectively question and resolve community challenges functioned as expected. However, organizations/networks, while essential, operated differently than originally hypothesized - not through formal organizations, but through diffuse family networks. Conclusions To date, few community mobilizing efforts in HIV prevention have clearly defined the meaning and domains of CM prior to intervention design. We distilled six CM domains from the literature; all were pertinent to mobilization in rural South Africa. While some adaptation of specific domains is required, they provide an extremely valuable organizational tool to guide CM programming and evaluation of critically needed mobilizing initiatives in Southern Africa. PMID:24147121

Inward open characterization of EmrD transporter with molecular dynamics simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Xianwei; Wang, Boxiong, E-mail: boxiong_wang@yahoo.com

EmrD is a member of the multidrug resistance exporter family. Up to now, little is known about the structural dynamics that underline the function of the EmrD protein in inward-facing open state and how the EmrD transits from an occluded state to an inward open state. For the first time the article applied the AT simulation to investigate the membrane transporter protein EmrD, and described the dynamic features of the whole protein, the domain, the helices, and the amino acid residues during an inward-open process from its occluded state. The gradual inward-open process is different from the current model ofmore » rigid-body domain motion in alternating-access mechanism. Simulation results show that the EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. In addition, it is observed that the helices exposed to the surrounding membrane show a higher level of flexibility than the other regions, and the protonated E227 plays a key role in the transition from the occluded to the open state. -- Highlights: •This study described the dynamic features of the whole EmrD protein, during an inward-open process from its occluded state. •The EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. •The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. •The protonated E227 plays a key role in the transition from the occluded to the open state.« less

Culturally Targeted Strategies for Diabetes Prevention in Minority Population.

PubMed

Lagisetty, Pooja A; Priyadarshini, Shubadra; Terrell, Stephanie; Hamati, Mary; Landgraf, Jessica; Chopra, Vineet; Heisler, Michele

2017-02-01

Purpose The purpose of this study is to (a) assess the effectiveness of culturally tailored diabetes prevention interventions in minority populations and (b) develop a novel framework to characterize 4 key domains of culturally tailored interventions. Prevention strategies specifically tailored to the culture of ethnic minority patients may help reduce the incidence of diabetes. Methods We searched PubMed, EMBASE, and CINAHL for English-language, randomized controlled trials (RCTs) or quasi-experimental (QE) trials testing culturally tailored interventions to prevent diabetes in minority populations. Two reviewers independently extracted data and assessed risk of bias. Inductive thematic analysis was used to develop a framework with 4 domains (FiLLM: Facilitating [ie, delivering] Interventions Through Language, Location, and Message). The framework was used to assess the overall effectiveness of culturally tailored interventions. Results Thirty-four trials met eligibility criteria. Twelve studies were RCTs, and 22 were QE trials. Twenty-five out of 34 studies (74%) that used cultural tailoring demonstrated significantly improved A1C, fasting glucose, and/or weight loss. Of the 25 successful interventions, 21 (84%) incorporated at least 3 culturally targeted domains. Seven studies used all 4 domains and were all successful. The least utilized domain was delivery (4/34) of the intervention's key educational message. Conclusions Culturally tailoring interventions across the 4 domains of facilitators, language, location, and messaging can be effective in improving risk factors for progression to diabetes among ethnic minority groups. Future studies should evaluate how specific tailoring approaches work compared to usual care as well as comparative effectiveness of each tailoring domain.

Multi-Domain Transfer Learning for Early Diagnosis of Alzheimer’s Disease

PubMed Central

Cheng, Bo; Liu, Mingxia; Li, Zuoyong

2017-01-01

Recently, transfer learning has been successfully applied in early diagnosis of Alzheimer’s Disease (AD) based on multi-domain data. However, most of existing methods only use data from a single auxiliary domain, and thus cannot utilize the intrinsic useful correlation information from multiple domains. Accordingly, in this paper, we consider the joint learning of tasks in multi-auxiliary domains and the target domain, and propose a novel Multi-Domain Transfer Learning (MDTL) framework for early diagnosis of AD. Specifically, the proposed MDTL framework consists of two key components: 1) a multi-domain transfer feature selection (MDTFS) model that selects the most informative feature subset from multi-domain data, and 2) a multidomain transfer classification (MDTC) model that can identify disease status for early AD detection. We evaluate our method on 807 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database using baseline magnetic resonance imaging (MRI) data. The experimental results show that the proposed MDTL method can effectively utilize multi-auxiliary domain data for improving the learning performance in the target domain, compared with several state-of-the-art methods. PMID:27928657

Listening in a Multilingual World: The Challenges of Second Language (L2) Listening

ERIC Educational Resources Information Center

Rost, Michael

2014-01-01

Research into language acquisition and oral language use was examined in order to identify key factors that contribute to the successful acquisition of second language (L2) listening ability. The factors were grouped into three major domains: affective, cognitive, and interpersonal. It is claimed that in each domain, proficient L2 listeners have…

Urban Third Grade Teachers' Practices and Perceptions in Science Instruction with English Language Learners

ERIC Educational Resources Information Center

Lewis, Scott; Maerten-Rivera, Jaime; Adamson, Karen; Lee, Okhee

2011-01-01

The study examined relationships among key domains of science instruction with English language learning (ELL) students based on teachers' perceptions of their classroom practices (i.e., what they think they do) and actual classroom practices (i.e., what they are observed doing). The four domains under investigation included: (1) teachers'…

Separating the Wheat from the Chaff: Identifying Key Elements in the NLA .AU Domain Harvest

ERIC Educational Resources Information Center

Fellows, Geoff; Harvey, Ross; Lloyd, Annemaree; Pymm, Bob; Wallis, Jake

2008-01-01

In 2005 and 2006 the National Library of Australia (NLA) carried out two whole-domain web harvests which complement the selective web archiving approach taken by PANDORA. Web harvests of this size pose significant challenges to their use. Despite these challenges, such harvests present fascinating research opportunities. The NLA has provided…

Investigating Key Psychometric Properties of the French Version of the Early Years Evaluation-Teacher Assessment

ERIC Educational Resources Information Center

Laurie, Robert; Sloat, Elizabeth

2016-01-01

This research investigates key psychometric properties of the French Early Years Evaluation-Teacher Assessment measure designed to systematically assess kindergarten children across five social and academic developmental domains: awareness of self and environment, social skills and behaviour, cognitive abilities, language and communication, and…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xianjun; Zhao, Fei; Wu, Yiran

Here, the Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combiningmore » the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.« less

Gloss measurements and rugometric inspection in dental biomaterials

NASA Astrophysics Data System (ADS)

Fernández-Oliveras, Alicia; Costa, Manuel F. M.; Yebra, Ana; Rubiño, Manuel; Pérez, María. M.

2013-11-01

In dental applications, optimizing appearance is desirable and increasingly demanded by patients. The specular gloss is among the major appearance properties of dental biomaterials, and its relationship with surface roughness has been reported. Roughness and gloss are key surface aspects that complement each other. We have experimentally analyzed the specular gloss and surface roughness of two different types of dental-resin composites and pre-sintered and sintered zirconia ceramics. We have studied two shades of both composite types and two sintered zirconia ceramics: colored and uncolored. Moreover, a surface treatment was applied to one specimen of each dental resin. Gloss measurements were performed with a standardized reflectometer and the corresponding gloss percentages were calculated. All the samples were submitted to rugometric non-invasive inspection with the MICROTOP.06.MFC laser microtopographer in order to determine meaningful statistical parameters such as the average roughness (Ra) and the root-mean-square deviation (Rq). For a comparison of the different biomaterials, the uncertainties associated to the measure of the surface gloss and roughness were also determined. The differences between the two shades of both kinds of composites proved significant in the case of the roughness parameters but not for the specular gloss. The surface treatment applied to the dental-resin composites increased the average roughness but the changes in the specular gloss were significant only for the A2 enamel nano-composite. For the zirconia ceramic the sintered process resulted in an increase in the surface roughness with a decrease of the specular gloss, corroborating that the relationship between the gloss and the roughness shows the expected behavior.

Multiplexed neural recording along a single optical fiber via optical reflectometry

PubMed Central

Rodriques, Samuel G.; Marblestone, Adam H.; Scholvin, Jorg; Dapello, Joel; Sarkar, Deblina; Mankin, Max; Gao, Ruixuan; Wood, Lowell; Boyden, Edward S.

2016-01-01

Abstract. We introduce the design and theoretical analysis of a fiber-optic architecture for neural recording without contrast agents, which transduces neural electrical signals into a multiplexed optical readout. Our sensor design is inspired by electro-optic modulators, which modulate the refractive index of a waveguide by applying a voltage across an electro-optic core material. We estimate that this design would allow recording of the activities of individual neurons located at points along a 10-cm length of optical fiber with 40-μm axial resolution and sensitivity down to 100  μV using commercially available optical reflectometers as readout devices. Neural recording sites detect a potential difference against a reference and apply this potential to a capacitor. The waveguide serves as one of the plates of the capacitor, so charge accumulation across the capacitor results in an optical effect. A key concept of the design is that the sensitivity can be improved by increasing the capacitance. To maximize the capacitance, we utilize a microscopic layer of material with high relative permittivity. If suitable materials can be found—possessing high capacitance per unit area as well as favorable properties with respect to toxicity, optical attenuation, ohmic junctions, and surface capacitance—then such sensing fibers could, in principle, be scaled down to few-micron cross-sections for minimally invasive neural interfacing. We study these material requirements and propose potential material choices. Custom-designed multimaterial optical fibers, probed using a reflectometric readout, may, therefore, provide a powerful platform for neural sensing. PMID:27194640

Spectralon solar diffuser BRDF variation for NPP, JPSS J1 and J2

NASA Astrophysics Data System (ADS)

Murgai, Vijay; Johnson, Lindsay; Klein, Staci

2017-09-01

The Visible/Infrared Imaging Radiometer Suite (VIIRS) is a key sensor on the Suomi National Polar-orbiting Partnership (NPP) satellite as well as the upcoming Joint Polar Satellite System (JPSS). VIIRS collects Earth radiometric and imagery data in 22 spectral bands from 0.4 to 12.5 μm. Radiometric calibration of the reflective bands in the 0.4 to 2.5 μm wavelength range is performed by measuring the sunlight reflectance from Spectralon®. Reflected sun light is directly proportional to the Bidirectional Reflectance Distribution Function (BRDF) of the Spectralon. This paper presents the BRDF measurements of the Spectralon for JPSS J2 in the 0.4 - 1.63 μm wavelength using PASCAL (Polarization And Scatter Characterization Analysis of Lambertian materials) with an uncertainty better than 1.2%. PASCAL makes absolute measurements of the BRDF in an analogous fashion to the National Institute of Standards and Technology (NIST) Spectral Tri-function Automated Reflectance Reflectometer (STARR) facility. Unique additional features of this instrument include the ability to vary the sample elevation and roll / clock the sample about its normal, allowing measurement of BRDF in the as used geometry. Comparison of BRDF in the as used configuration for NPP, J1, and J2 shows variation of up to 3%. The sign of the change from panel to panel depends on the angle of incidence and view angle. The results demonstrate lot to lot variability in Spectralon and emphasize the necessity of characterizing each panel. A pattern in the BRDF variation is also presented.

Studies of electrochemical interfaces by TOF neutron reflectometry at the IBR-2 reactor

NASA Astrophysics Data System (ADS)

Petrenko, V. I.; Gapon, I. V.; Rulev, A. A.; Ushakova, E. E.; Kataev, E. Yu; Yashina, L. V.; Itkis, D. M.; Avdeev, M. V.

2018-03-01

The operation performance of electrochemical energy conversion and storage systems such as supercapacitors and batteries depends on the processes occurring at the electrochemical interfaces, where charge separation and chemical reactions occur. Here, we report about the tests of the neutron reflectometry cells specially designed for operando studies of structural changes at the electrochemical interfaces between solid electrodes and liquid electrolytes. The cells are compatible with anhydrous electrolytes with organic solvents, which are employed today in all lithium ion batteries and most supercapacitors. The sensitivity of neutron reflectometry applied at the time-of-flight (TOF) reflectometer at the pulsed reactor IBR-2 is discussed regarding the effect of solid electrolyte interphase (SEI) formation on metal electrode surface.

Calibration and standards beamline 6.3.2 at the ALS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Underwood, J.H.; Gullikson, E.M.; Koike, M.

1997-04-01

More sophisticated optics for the x-ray, soft x-ray and far ultraviolet spectral regions being developed for synchrotron radiation research and many other applications, require accurate calibration and standards facilities for measuring reflectivity of mirrors and multilayer coatings, transmission of thin films, bandpass of multilayers, efficiency of gratings or detectors, etc. For this purpose beamline 6.3.2 was built at the ALS. Its energy coverage, versatility, simplicity and convenience also make it useful for a wide range of other experiments. The paper describes the components of this beamline, consisting of: a four jaw aperture; a horizontal focusing mirror; a monochromator; exit slit;more » vertical focusing mirror; mechanical and vacuum system; reflectometer; filter wheels; and data acquisition system.« less

An uncertainty budget for VHF and UHF reflectometers

NASA Astrophysics Data System (ADS)

Ridler, N. M.; Medley, C. J.

1992-05-01

Details of the derivation of an uncertainty budget for one port immittance or complex voltage reflection coefficient measuring instruments, operating at VHF and UHF in the 14 mm 50 ohm coaxial line size, are reported. The principles of the uncertainty budget are given along with experimental results obtained using six ports and a network analyzer as the measuring instruments. Details of the types of calibration for which the uncertainty budget is suitable are reported. Various aspects of the uncertainty budget are considered and general principles and treatment of the type A and type B contributions are discussed. Experimental results obtained using the uncertainty budget are given. A summary of uncertainties for the six ports and HP8753B automatic network analyzer are also given.

An accurate automated technique for quasi-optics measurement of the microwave diagnostics for fusion plasma

NASA Astrophysics Data System (ADS)

Hu, Jianqiang; Liu, Ahdi; Zhou, Chu; Zhang, Xiaohui; Wang, Mingyuan; Zhang, Jin; Feng, Xi; Li, Hong; Xie, Jinlin; Liu, Wandong; Yu, Changxuan

2017-08-01

A new integrated technique for fast and accurate measurement of the quasi-optics, especially for the microwave/millimeter wave diagnostic systems of fusion plasma, has been developed. Using the LabVIEW-based comprehensive scanning system, we can realize not only automatic but also fast and accurate measurement, which will help to eliminate the effects of temperature drift and standing wave/multi-reflection. With the Matlab-based asymmetric two-dimensional Gaussian fitting method, all the desired parameters of the microwave beam can be obtained. This technique can be used in the design and testing of microwave diagnostic systems such as reflectometers and the electron cyclotron emission imaging diagnostic systems of the Experimental Advanced Superconducting Tokamak.

Grazing incidence reflection coefficients of rhodium, osmium, platinum, and gold from 50 to 300 A

NASA Technical Reports Server (NTRS)

Hettrick, M. C.; Edelstein, J.; Flint, S. A.

1985-01-01

Reflectance measurements were made of several metals illuminated from various angles with light at 14 wavelengths in the interval 46.5-283 A. The metals, Rh, Os, Pt and Au were deposited as 125 A films on a binding substrate through electron beam epitaxy. Measurements were made with a grazing incidence monochromator and a reflectometer. The data generally showed lowered reflectance with increasing angles of illumination and shorter wavelengths. The reflectance peak, however, was located at wavelengths of 100-160 A, particularly at large grazing incidences. The wavelengths correspond with the 5p to epsilon-d transition in all of the elements. Rh displayed the highest overall reflectance, and both Rh and Os were more efficient than Au or Pt.

Mutations in the FMN domain modulate MCD spectra of the heme site in the oxygenase domain of inducible nitric oxide synthase.

PubMed

Sempombe, Joseph; Elmore, Bradley O; Sun, Xi; Dupont, Andrea; Ghosh, Dipak K; Guillemette, J Guy; Kirk, Martin L; Feng, Changjian

2009-05-27

The nitric oxide synthase (NOS) output state for NO production is a complex of the flavin mononucleotide (FMN)-binding domain and the heme domain, and thereby it facilitates the interdomain electron transfer from the FMN to the catalytic heme site. Emerging evidence suggests that interdomain FMN-heme interactions are important in the formation of the output state because they guide the docking of the FMN domain to the heme domain. In this study, notable effects of mutations in the adjacent FMN domain on the heme structure in a human iNOS bidomain oxygenase/FMN construct have been observed by using low-temperature magnetic circular dichroism (MCD) spectroscopy. The comparative MCD study of wild-type and mutant proteins clearly indicates that a properly docked FMN domain contributes to the observed L-Arg perturbation of the heme MCD spectrum in the wild-type protein and that the conserved surface residues in the FMN domain (E546 and E603) play key roles in facilitating a productive alignment of the FMN and heme domains in iNOS.

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

DOE PAGES

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; ...

2017-05-17

Here, the Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combiningmore » the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.« less

Mutations in the LRRK2 Roc-COR tandem domain link Parkinson's disease to Wnt signalling pathways.

PubMed

Sancho, Rosa M; Law, Bernard M H; Harvey, Kirsten

2009-10-15

Mutations in PARK8, encoding LRRK2, are the most common known cause of Parkinson's disease. The LRRK2 Roc-COR tandem domain exhibits GTPase activity controlling LRRK2 kinase activity via an intramolecular process. We report the interaction of LRRK2 with the dishevelled family of phosphoproteins (DVL1-3), key regulators of Wnt (Wingless/Int) signalling pathways important for axon guidance, synapse formation and neuronal maintenance. Interestingly, DVLs can interact with and mediate the activation of small GTPases with structural similarity to the LRRK2 Roc domain. The LRRK2 Roc-COR domain and the DVL1 DEP domain were necessary and sufficient for LRRK2-DVL1 interaction. Co-expression of DVL1 increased LRRK2 steady-state protein levels, an effect that was dependent on the DEP domain. Strikingly, LRRK2-DVL1-3 interactions were disrupted by the familial PARK8 mutation Y1699C, whereas pathogenic mutations at residues R1441 and R1728 strengthened LRRK2-DVL1 interactions. Co-expression of DVL1 with LRRK2 in mammalian cells resulted in the redistribution of LRRK2 to typical cytoplasmic DVL1 aggregates in HEK293 and SH-SY5Y cells and co-localization in neurites and growth cones of differentiated dopaminergic SH-SY5Y cells. This is the first report of the modulation of a key LRRK2-accessory protein interaction by PARK8 Roc-COR domain mutations segregating with Parkinson's disease. Since the DVL1 DEP domain is known to be involved in the regulation of small GTPases, we propose that: (i) DVLs may influence LRRK2 GTPase activity, and (ii) Roc-COR domain mutations modulating LRRK2-DVL interactions indirectly influence kinase activity. Our findings also link LRRK2 to Wnt signalling pathways, suggesting novel pathogenic mechanisms and new targets for genetic analysis in Parkinson's disease.

Mutations in the LRRK2 Roc-COR tandem domain link Parkinson's disease to Wnt signalling pathways

PubMed Central

Sancho, Rosa M.; Law, Bernard M.H.; Harvey, Kirsten

2009-01-01

Mutations in PARK8, encoding LRRK2, are the most common known cause of Parkinson's disease. The LRRK2 Roc-COR tandem domain exhibits GTPase activity controlling LRRK2 kinase activity via an intramolecular process. We report the interaction of LRRK2 with the dishevelled family of phosphoproteins (DVL1-3), key regulators of Wnt (Wingless/Int) signalling pathways important for axon guidance, synapse formation and neuronal maintenance. Interestingly, DVLs can interact with and mediate the activation of small GTPases with structural similarity to the LRRK2 Roc domain. The LRRK2 Roc-COR domain and the DVL1 DEP domain were necessary and sufficient for LRRK2–DVL1 interaction. Co-expression of DVL1 increased LRRK2 steady-state protein levels, an effect that was dependent on the DEP domain. Strikingly, LRRK2–DVL1-3 interactions were disrupted by the familial PARK8 mutation Y1699C, whereas pathogenic mutations at residues R1441 and R1728 strengthened LRRK2–DVL1 interactions. Co-expression of DVL1 with LRRK2 in mammalian cells resulted in the redistribution of LRRK2 to typical cytoplasmic DVL1 aggregates in HEK293 and SH-SY5Y cells and co-localization in neurites and growth cones of differentiated dopaminergic SH-SY5Y cells. This is the first report of the modulation of a key LRRK2-accessory protein interaction by PARK8 Roc-COR domain mutations segregating with Parkinson's disease. Since the DVL1 DEP domain is known to be involved in the regulation of small GTPases, we propose that: (i) DVLs may influence LRRK2 GTPase activity, and (ii) Roc-COR domain mutations modulating LRRK2–DVL interactions indirectly influence kinase activity. Our findings also link LRRK2 to Wnt signalling pathways, suggesting novel pathogenic mechanisms and new targets for genetic analysis in Parkinson's disease. PMID:19625296

A Comparison between 2010 and 2006 Air Quality and Meteorological Conditions, andEmissions and Boundary Conditions used in Simulations of the AQMEII-2 North American Domain

EPA Science Inventory

Several participants in Phase 2 of the Air Quality Model Evaluation International Initiative (AQMEII-2) who are applying coupled models to the North American domain are comparing model results for two years: 2006 and 2010. While a key difference of interest between these two yea...

Research on Agriculture Domain Meta-Search Engine System

NASA Astrophysics Data System (ADS)

Xie, Nengfu; Wang, Wensheng

The rapid growth of agriculture web information brings a fact that search engine can not return a satisfied result for users’ queries. In this paper, we propose an agriculture domain search engine system, called ADSE, that can obtains results by an advance interface to several searches and aggregates them. We also discuss two key technologies: agriculture information determination and engine.

Functional hierarchy of the N-terminal tyrosines of SLP-76.

PubMed

Jordan, Martha S; Sadler, Jeffrey; Austin, Jessica E; Finkelstein, Lisa D; Singer, Andrew L; Schwartzberg, Pamela L; Koretzky, Gary A

2006-02-15

The adaptor protein Src homology 2 domain-containing leukocyte phosphoprotein of 76 kDa (SLP-76) plays a central role in T cell activation and T cell development. SLP-76 has three functional modules: an acidic domain with three key tyrosines, a central proline-rich domain, and a C-terminal Src homology 2 domain. Of these, mutation of the three N-terminal tyrosines (Y112, Y128, and Y145) results in the most profound effects on T cell development and function. Y112 and Y128 associate with Vav and Nck, two proteins shown to be important for TCR-induced phosphorylation of proximal signaling substrates, Ca(2+) flux, and actin reorganization. Y145 has been shown to be important for optimal association of SLP-76 with inducible tyrosine kinase, a key regulator of T cell function. To investigate further the role of the phosphorylatable tyrosines of SLP-76 in TCR signaling, cell lines and primary T cells expressing SLP-76 with mutations in individual or paired tyrosine residues were analyzed. These studies show that Tyr(145) of SLP-76 is the most critical tyrosine for both T cell function in vitro and T cell development in vivo.

BARI+: A Biometric Based Distributed Key Management Approach for Wireless Body Area Networks

PubMed Central

Muhammad, Khaliq-ur-Rahman Raazi Syed; Lee, Heejo; Lee, Sungyoung; Lee, Young-Koo

2010-01-01

Wireless body area networks (WBAN) consist of resource constrained sensing devices just like other wireless sensor networks (WSN). However, they differ from WSN in topology, scale and security requirements. Due to these differences, key management schemes designed for WSN are inefficient and unnecessarily complex when applied to WBAN. Considering the key management issue, WBAN are also different from WPAN because WBAN can use random biometric measurements as keys. We highlight the differences between WSN and WBAN and propose an efficient key management scheme, which makes use of biometrics and is specifically designed for WBAN domain. PMID:22319333

BARI+: a biometric based distributed key management approach for wireless body area networks.

PubMed

Muhammad, Khaliq-ur-Rahman Raazi Syed; Lee, Heejo; Lee, Sungyoung; Lee, Young-Koo

2010-01-01

Wireless body area networks (WBAN) consist of resource constrained sensing devices just like other wireless sensor networks (WSN). However, they differ from WSN in topology, scale and security requirements. Due to these differences, key management schemes designed for WSN are inefficient and unnecessarily complex when applied to WBAN. Considering the key management issue, WBAN are also different from WPAN because WBAN can use random biometric measurements as keys. We highlight the differences between WSN and WBAN and propose an efficient key management scheme, which makes use of biometrics and is specifically designed for WBAN domain.

Key Ideas: What Are They and How Can They Help Us Understand How People View Proof?

ERIC Educational Resources Information Center

Raman, Manya

2003-01-01

Examines the views of proof held by university-level mathematics students and teachers. Develops a framework for characterizing people's views of proof based on a distinction between public and private aspects of proof and the key ideas that link these two domains. (Author/KHR)

Knowledge Maps for E-Learning

ERIC Educational Resources Information Center

Lee, Jae Hwa; Segev, Aviv

2012-01-01

Maps such as concept maps and knowledge maps are often used as learning materials. These maps have nodes and links, nodes as key concepts and links as relationships between key concepts. From a map, the user can recognize the important concepts and the relationships between them. To build concept or knowledge maps, domain experts are needed.…

America's Children: Key National Indicators of Well-Being. 2009

ERIC Educational Resources Information Center

Blachman, Dara; Laughlin, Lynda; Lukacs, Susan; Pastor, Patricia; Howie, LaJeana; Sonnenberg, William; Axelrad, Daniel; Steffen, Barry; Baum, Katrina; Lopez, Marsha; Jekielek, Susan; Nord, Mark; Morisi, Teri; Avenevoli, Shelli; Singleton, James; Colpe, Lisa; Fungwe, Thomas; Ghandour, Reem

2009-01-01

"America's Children: Key National Indicators of Well-Being" provides annual updates on the well-being of children and families in the United States across a range of domains. A more detailed report alternates every other year with a condensed version that highlights selected indicators. This year, the Forum is publishing the full report…

Scattering Theory for the Acoustic Wave Equation in an Arbitrary Exterior Domain

DTIC Science & Technology

1976-08-30

65) will be further studied in the follow-up article. REFERENCES 1. C.H. Wilcox, Scattering Theory for the d - Alembert Equation in Exterior Domains...Exterior Domain Naval Research Lab Washington D C 30 Aug 76 254060 NRL Report 8030 Scattering Theory for the Acoustic Wave SEquation in an Arbitrary...STATEMENT (of the .b.Ia te ntere., d in loc k 10. If diferegn from R pr)A. 16 SUPPLEMENTARY NOTES IS KEY WORDS (Co.n.v onl r*eers Od*e ifftoneemy and

Chronic disease management in children based on the five domains of health.

PubMed

So, Wing Lung Alvin

2013-01-01

Through a case study of a child with cystic fibrosis, the interactions among various domains of health have been discussed-namely, biomedical, physical, psychological/behavioural, and social. In pediatrics, development is another key domain relevant to the management of a chronic disease. An individualised management plan for this case has been outlined, and consideration of this framework may be worthwhile when managing other paediatric patients with chronic disease. Patient empowerment and parental education, as well as good co-ordination of health service delivery, are imperative to holistic patient care.

Design and Implementation of a Prototype Microcomputer Database Management System for the Standardization of Data Elements for the Department of Defense

DTIC Science & Technology

1990-09-01

Justification Cat: Left Timeliness Identifier: Qwe (FI] Domain I Def Text: -Press [F3 to nove in/out of the fields below. Use ARROW keys to scroll- Rec: Host...Delete a record Elemont Creator ID: Justification Cat: Left Timeliness Identifier: Qwe [FI) Domain Def Text: - Press (F3) to move in/out of the...Number: 1 Alias Name: Accounting Code Data Value Type ID: QL Max Length Characters: 34 Timeliness ID: Qwe Justification Category: Left Creator ID: Domain

The Digital Thread as the Key Enabler

DTIC Science & Technology

2016-11-01

17 Defense AT&L: November-December 2016 The Digital Thread as the Key Enabler Col. Keith Bearden, USAF Bearden is the deputy director of...enabling you to do your job better, faster and cheaper. There is one initiative, the key enabler, to accomplish this goal—the digital thread . But let’s... process that would allow for rapid cross- domain analysis and technology transition prior to bending metal. • Re-establish a culture of “hands-on

Incorporating World Knowledge to Document Clustering via Heterogeneous Information Networks.

PubMed

Wang, Chenguang; Song, Yangqiu; El-Kishky, Ahmed; Roth, Dan; Zhang, Ming; Han, Jiawei

2015-08-01

One of the key obstacles in making learning protocols realistic in applications is the need to supervise them, a costly process that often requires hiring domain experts. We consider the framework to use the world knowledge as indirect supervision. World knowledge is general-purpose knowledge, which is not designed for any specific domain. Then the key challenges are how to adapt the world knowledge to domains and how to represent it for learning. In this paper, we provide an example of using world knowledge for domain dependent document clustering. We provide three ways to specify the world knowledge to domains by resolving the ambiguity of the entities and their types, and represent the data with world knowledge as a heterogeneous information network. Then we propose a clustering algorithm that can cluster multiple types and incorporate the sub-type information as constraints. In the experiments, we use two existing knowledge bases as our sources of world knowledge. One is Freebase, which is collaboratively collected knowledge about entities and their organizations. The other is YAGO2, a knowledge base automatically extracted from Wikipedia and maps knowledge to the linguistic knowledge base, Word-Net. Experimental results on two text benchmark datasets (20newsgroups and RCV1) show that incorporating world knowledge as indirect supervision can significantly outperform the state-of-the-art clustering algorithms as well as clustering algorithms enhanced with world knowledge features.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mei, Yang; Glover, Karen; Su, Minfei

BECN1 (Beclin 1), a highly conserved eukaryotic protein, is a key regulator of autophagy, a cellular homeostasis pathway, and also participates in vacuolar protein sorting, endocytic trafficking, and apoptosis. BECN1 is important for embryonic development, the innate immune response, tumor suppression, and protection against neurodegenerative disorders, diabetes, and heart disease. BECN1 mediates autophagy as a core component of the class III phosphatidylinositol 3-kinase complexes. However, the exact mechanism by which it regulates the activity of these complexes, or mediates its other diverse functions is unclear. BECN1 interacts with several diverse protein partners, perhaps serving as a scaffold or interaction hubmore » for autophagy. Based on extensive structural, biophysical and bioinformatics analyses, BECN1 consists of an intrinsically disordered region (IDR), which includes a BH3 homology domain (BH3D); a flexible helical domain (FHD); a coiled-coil domain (CCD); and a β-α-repeated autophagy-specific domain (BARAD). Each of these BECN1 domains mediates multiple diverse interactions that involve concomitant conformational changes. Thus, BECN1 conformational flexibility likely plays a key role in facilitating diverse protein interactions. Further, BECN1 conformation and interactions are also modulated by numerous post-translational modifications. A better structure-based understanding of the interplay between different BECN1 conformational and binding states, and the impact of post-translational modifications will be essential to elucidating the mechanism of its multiple biological roles.« less

Incorporating World Knowledge to Document Clustering via Heterogeneous Information Networks

PubMed Central

Wang, Chenguang; Song, Yangqiu; El-Kishky, Ahmed; Roth, Dan; Zhang, Ming; Han, Jiawei

2015-01-01

One of the key obstacles in making learning protocols realistic in applications is the need to supervise them, a costly process that often requires hiring domain experts. We consider the framework to use the world knowledge as indirect supervision. World knowledge is general-purpose knowledge, which is not designed for any specific domain. Then the key challenges are how to adapt the world knowledge to domains and how to represent it for learning. In this paper, we provide an example of using world knowledge for domain dependent document clustering. We provide three ways to specify the world knowledge to domains by resolving the ambiguity of the entities and their types, and represent the data with world knowledge as a heterogeneous information network. Then we propose a clustering algorithm that can cluster multiple types and incorporate the sub-type information as constraints. In the experiments, we use two existing knowledge bases as our sources of world knowledge. One is Freebase, which is collaboratively collected knowledge about entities and their organizations. The other is YAGO2, a knowledge base automatically extracted from Wikipedia and maps knowledge to the linguistic knowledge base, Word-Net. Experimental results on two text benchmark datasets (20newsgroups and RCV1) show that incorporating world knowledge as indirect supervision can significantly outperform the state-of-the-art clustering algorithms as well as clustering algorithms enhanced with world knowledge features. PMID:26705504

The intervening domain from MeCP2 enhances the DNA affinity of the methyl binding domain and provides an independent DNA interaction site.

PubMed

Claveria-Gimeno, Rafael; Lanuza, Pilar M; Morales-Chueca, Ignacio; Jorge-Torres, Olga C; Vega, Sonia; Abian, Olga; Esteller, Manel; Velazquez-Campoy, Adrian

2017-01-31

Methyl-CpG binding protein 2 (MeCP2) preferentially interacts with methylated DNA and it is involved in epigenetic regulation and chromatin remodelling. Mutations in MeCP2 are linked to Rett syndrome, the leading cause of intellectual retardation in girls and causing mental, motor and growth impairment. Unstructured regions in MeCP2 provide the plasticity for establishing interactions with multiple binding partners. We present a biophysical characterization of the methyl binding domain (MBD) from MeCP2 reporting the contribution of flanking domains to its structural stability and dsDNA interaction. The flanking disordered intervening domain (ID) increased the structural stability of MBD, modified its dsDNA binding profile from an entropically-driven moderate-affinity binding to an overwhelmingly enthalpically-driven high-affinity binding. Additionally, ID provided an additional site for simultaneously and autonomously binding an independent dsDNA molecule, which is a key feature linked to the chromatin remodelling and looping activity of MeCP2, as well as its ability to interact with nucleosomes replacing histone H1. The dsDNA interaction is characterized by an unusually large heat capacity linked to a cluster of water molecules trapped within the binding interface. The dynamics of disordered regions together with extrinsic factors are key determinants of MeCP2 global structural properties and functional capabilities.

The intervening domain from MeCP2 enhances the DNA affinity of the methyl binding domain and provides an independent DNA interaction site

PubMed Central

Claveria-Gimeno, Rafael; Lanuza, Pilar M.; Morales-Chueca, Ignacio; Jorge-Torres, Olga C.; Vega, Sonia; Abian, Olga; Esteller, Manel; Velazquez-Campoy, Adrian

2017-01-01

Methyl-CpG binding protein 2 (MeCP2) preferentially interacts with methylated DNA and it is involved in epigenetic regulation and chromatin remodelling. Mutations in MeCP2 are linked to Rett syndrome, the leading cause of intellectual retardation in girls and causing mental, motor and growth impairment. Unstructured regions in MeCP2 provide the plasticity for establishing interactions with multiple binding partners. We present a biophysical characterization of the methyl binding domain (MBD) from MeCP2 reporting the contribution of flanking domains to its structural stability and dsDNA interaction. The flanking disordered intervening domain (ID) increased the structural stability of MBD, modified its dsDNA binding profile from an entropically-driven moderate-affinity binding to an overwhelmingly enthalpically-driven high-affinity binding. Additionally, ID provided an additional site for simultaneously and autonomously binding an independent dsDNA molecule, which is a key feature linked to the chromatin remodelling and looping activity of MeCP2, as well as its ability to interact with nucleosomes replacing histone H1. The dsDNA interaction is characterized by an unusually large heat capacity linked to a cluster of water molecules trapped within the binding interface. The dynamics of disordered regions together with extrinsic factors are key determinants of MeCP2 global structural properties and functional capabilities. PMID:28139759

Suppressor of cytokine signaling 1 interacts with oncogenic lymphocyte-specific protein tyrosine kinase.

PubMed

Venkitachalam, Srividya; Chueh, Fu-Yu; Leong, King-Fu; Pabich, Samantha; Yu, Chao-Lan

2011-03-01

Lymphocyte-specific protein tyrosine kinase (Lck) plays a key role in T cell signal transduction and is tightly regulated by phosphorylation and dephosphorylation. Lck can function as an oncoprotein when overexpressed or constantly activated by mutations. Our previous studies showed that Lck-induced cellular transformation could be suppressed by enforced expression of suppressor of cytokine signaling 1 (SOCS1), a SOCS family member involved in the negative feedback control of cytokine signaling. We observed attenuated Lck kinase activity in SOCS1-expressing cells, suggesting an important role of SOCS in regulating Lck functions. It remains largely unknown whether and how SOCS proteins interact with the oncogenic Lck kinase. Here, we report that among four SOCS family proteins, SOCS1, SOCS2, SOCS3 and CIS (cytokine-inducible SH2 domain containing protein), SOCS1 has the highest affinity in binding to the oncogenic Lck kinase. We identified the positive regulatory phosphotyrosine 394 residue in the kinase domain as the key interacting determinant in Lck. Additionally, the Lck kinase domain alone is sufficient to bind SOCS1. While the SH2 domain in SOCS1 is important in its association with the oncogenic Lck kinase, other functional domains may also contribute to overall binding affinity. These findings provide important mechanistic insights into the role of SOCS proteins as tumor suppressors in cells transformed by oncogenic protein tyrosine kinases.

Suppressor of cytokine signaling 1 interacts with oncogenic lymphocyte-specific protein tyrosine kinase

PubMed Central

VENKITACHALAM, SRIVIDYA; CHUEH, FU-YU; LEONG, KING-FU; PABICH, SAMANTHA; YU, CHAO-LAN

2011-01-01

Lymphocyte-specific protein tyrosine kinase (Lck) plays a key role in T cell signal transduction and is tightly regulated by phosphorylation and dephosphorylation. Lck can function as an oncoprotein when overexpressed or constantly activated by mutations. Our previous studies showed that Lck-induced cellular transformation could be suppressed by enforced expression of suppressor of cytokine signaling 1 (SOCS1), a SOCS family member involved in the negative feedback control of cytokine signaling. We observed attenuated Lck kinase activity in SOCS1-expressing cells, suggesting an important role of SOCS in regulating Lck functions. It remains largely unknown whether and how SOCS proteins interact with the oncogenic Lck kinase. Here we report that, among four SOCS family proteins, SOCS1, SOCS2, SOCS3 and CIS (cytokine–inducible SH2 domain containing protein), SOCS1 has the highest affinity in binding to the oncogenic Lck kinase. We identify the positive regulatory phospho-tyrosine 394 residue in the kinase domain as the key interacting determinant in Lck. Additionally, the Lck kinase domain alone is sufficient to bind SOCS1. While the SH2 domain in SOCS1 is important in its association with the oncogenic Lck kinase, other functional domains may also contribute to overall binding affinity. These findings provide important mechanistic insights into the role of SOCS proteins as tumor suppressors in cells transformed by oncogenic protein tyrosine kinases. PMID:21234523

Culturally Targeted Strategies for Diabetes Prevention in Minority Populations: A Systematic Review and Framework

PubMed Central

Lagisetty, Pooja A.; Priyadarshini, Shubadra; Terrell, Stephanie; Hamati, Mary; Landgraf, Jessica; Chopra, Vineet; Heisler, Michele

2017-01-01

Purpose The purpose of this study is to (a) assess the effectiveness of culturally tailored diabetes prevention interventions in minority populations and (b) develop a novel framework to characterize four key domains of culturally tailored interventions. Prevention strategies specifically tailored to the culture of ethnic minority patients may help reduce the incidence of diabetes. Methods We searched PubMed, EMBASE, and CINAHL for English-language, randomized controlled trials (RCTs) or quasi-experimental (QE) trials testing culturally tailored interventions to prevent diabetes in minority populations. Two reviewers independently extracted data and assessed risk of bias. Inductive thematic analysis was used to develop a framework with four domains (FiLLM: Facilitating [i.e., delivering] Interventions through Language, Location and Message). The framework was used to assess the overall effectiveness of culturally tailored interventions. Results Thirty-four trials met eligibility criteria. Twelve studies were randomized controlled trials, and 22 were quasi-experimental trials. Twenty-five out of 34 studies (74%) that used cultural tailoring demonstrated significantly improved Hemoglobin A1C, fasting glucose, and/or weight loss. Of the 25 successful interventions, 21 (84%) incorporated at least three culturally targeted domains. Seven studies used all four domains and were all successful. The least utilized domain was delivery (4/34) of the intervention’s key educational message. Conclusions Culturally tailoring interventions across the four domains of facilitators, language, location, and messaging can be effective in improving risk factors for progression to diabetes among ethnic minority groups. Future studies should evaluate how specific tailoring approaches work compared to usual care as well as comparative effectiveness of each tailoring domain. Registration (PROSPERO registration: CRD42015016914) PMID:28118127

Dimer formation through domain swapping in the crystal structure of the Grb2-SH2-Ac-pYVNV complex.

PubMed

Schiering, N; Casale, E; Caccia, P; Giordano, P; Battistini, C

2000-11-07

Src homology 2 (SH2) domains are key modules in intracellular signal transduction. They link activated cell surface receptors to downstream targets by binding to phosphotyrosine-containing sequence motifs. The crystal structure of a Grb2-SH2 domain-phosphopeptide complex was determined at 2.4 A resolution. The asymmetric unit contains four polypeptide chains. There is an unexpected domain swap so that individual chains do not adopt a closed SH2 fold. Instead, reorganization of the EF loop leads to an open, nonglobular fold, which associates with an equivalent partner to generate an intertwined dimer. As in previously reported crystal structures of canonical Grb2-SH2 domain-peptide complexes, each of the four hybrid SH2 domains in the two domain-swapped dimers binds the phosphopeptide in a type I beta-turn conformation. This report is the first to describe domain swapping for an SH2 domain. While in vivo evidence of dimerization of Grb2 exists, our SH2 dimer is metastable and a physiological role of this new form of dimer formation remains to be demonstrated.

The Design and Development of a Potent and Selective Novel Diprolyl Derivative That Binds to the N-Domain of Angiotensin-I Converting Enzyme.

PubMed

Fienberg, Stephen; Cozier, Gyles E; Acharya, K Ravi; Chibale, Kelly; Sturrock, Edward D

2018-01-11

Angiotensin-I converting enzyme (ACE) is a zinc metalloprotease consisting of two catalytic domains (N- and C-). Most clinical ACE inhibitor(s) (ACEi) have been shown to inhibit both domains nonselectively, resulting in adverse effects such as cough and angioedema. Selectively inhibiting the individual domains is likely to reduce these effects and potentially treat fibrosis in addition to hypertension. ACEi from the GVK Biosciences database were inspected for possible N-domain selective binding patterns. From this set, a diprolyl chemical series was modeled using docking simulations. The series was expanded based on key target interactions involving residues known to impart N-domain selectivity. In total, seven diprolyl compounds were synthesized and tested for N-domain selective ACE inhibition. One compound with an aspartic acid in the P 2 position (compound 16) displayed potent inhibition (K i = 11.45 nM) and was 84-fold more selective toward the N-domain. A high-resolution crystal structure of compound 16 in complex with the N-domain revealed the molecular basis for the observed selectivity.

A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies.

PubMed

Zahn, Raphael; Osmanović, Dino; Ehret, Severin; Araya Callis, Carolina; Frey, Steffen; Stewart, Murray; You, Changjiang; Görlich, Dirk; Hoogenboom, Bart W; Richter, Ralf P

2016-04-08

The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior - a key element for the transport selectivity of the NPC - was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface.

Remote-sensing image encryption in hybrid domains

NASA Astrophysics Data System (ADS)

Zhang, Xiaoqiang; Zhu, Guiliang; Ma, Shilong

2012-04-01

Remote-sensing technology plays an important role in military and industrial fields. Remote-sensing image is the main means of acquiring information from satellites, which always contain some confidential information. To securely transmit and store remote-sensing images, we propose a new image encryption algorithm in hybrid domains. This algorithm makes full use of the advantages of image encryption in both spatial domain and transform domain. First, the low-pass subband coefficients of image DWT (discrete wavelet transform) decomposition are sorted by a PWLCM system in transform domain. Second, the image after IDWT (inverse discrete wavelet transform) reconstruction is diffused with 2D (two-dimensional) Logistic map and XOR operation in spatial domain. The experiment results and algorithm analyses show that the new algorithm possesses a large key space and can resist brute-force, statistical and differential attacks. Meanwhile, the proposed algorithm has the desirable encryption efficiency to satisfy requirements in practice.

Domain Specific Language Support for Exascale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mellor-Crummey, John

A multi-institutional project known as D-TEC (short for “Domain- specific Technology for Exascale Computing”) set out to explore technologies to support the construction of Domain Specific Languages (DSLs) to map application programs to exascale architectures. DSLs employ automated code transformation to shift the burden of delivering portable performance from application programmers to compilers. Two chief properties contribute: DSLs permit expression at a high level of abstraction so that a programmer’s intent is clear to a compiler and DSL implementations encapsulate human domain-specific optimization knowledge so that a compiler can be smart enough to achieve good results on specific hardware. Domainmore » specificity is what makes these properties possible in a programming language. If leveraging domain specificity is the key to keep exascale software tractable, a corollary is that many different DSLs will be needed to encompass the full range of exascale computing applications; moreover, a single application may well need to use several different DSLs in conjunction. As a result, developing a general toolkit for building domain-specific languages was a key goal for the D-TEC project. Different aspects of the D-TEC research portfolio were the focus of work at each of the partner institutions in the multi-institutional project. D-TEC research and development work at Rice University focused on on three principal topics: understanding how to automate the tuning of code for complex architectures, research and development of the Rosebud DSL engine, and compiler technology to support complex execution platforms. This report provides a summary of the research and development work on the D-TEC project at Rice University.« less

Older adults' perspectives on key domains of childhood social and economic experiences and opportunities: a first step to creating a multidimensional measure

PubMed Central

Yen, Irene H; Stewart, Anita L; Scherzer, Teresa; Pérez-Stable, Eliseo J

2007-01-01

Objectives Although research has found that childhood socioeconomic status (SES) is associated with physical and mental health in mid- and later life, most of these studies used conventional, single dimension SES measures for the childhood period such as household income or educational attainment of parents. Life course and health disparities research would benefit from identification and measurement of a variety of childhood social and economic experiences and opportunities that might affect health in later life. Design This study utilized qualitative research methods to identify key dimensions of childhood experiences related to SES. We conducted in-depth interviews with 25 adults age 55 to 80 years from diverse economic and ethnic backgrounds. Topics included home, neighborhood, school, and work experiences during early childhood and adolescence. Interviews were audio-taped and transcripts were coded to identify thematic domains. Results We identified eight thematic domains, many of which had clear subdomains: home and family circumstances, neighborhood, work and money, potential for advancement through schooling, school quality and content, discrimination, influence and support of adults, and leisure activities. These domains highlight individual characteristics and experiences and also economic and educational opportunities. Conclusion These domains of childhood social and economic circumstances add breadth and depth to conventional conceptualization of childhood SES. When the domains are translated into a measurement tool, it will allow for the possibility of classifying people along multiple dimensions, such as from a low economic circumstance with high levels of adult support. PMID:17986341

Professional Competence of Prospective Teachers in Business and Economics Education: Evaluation of a Competence Model Using Structural Equation Modeling

ERIC Educational Resources Information Center

Bouley, Franziska; Wuttke, Eveline; Schnick-Vollmer, Kathleen; Schmitz, Bernhard; Berger, Stefanie; Fritsch, Sabine; Seifried, Jürgen

2015-01-01

Teacher competence is crucial for quality of teaching and learner achievement. Competency models and competence measurement are prevalent in domains such as the natural sciences and lacking in others. We conducted our research in the field of business and economics education by focusing on the accounting domain because it is key to a deep…

Self-Esteem Is Relatively Stable Late in Life: The Role of Resources in the Health, Self-Regulation, and Social Domains

ERIC Educational Resources Information Center

Wagner, Jenny; Hoppmann, Christiane; Ram, Nilam; Gerstorf, Denis

2015-01-01

A large body of research has documented changes in self-esteem across adulthood and individual-difference correlates thereof. However, little is known about whether people maintain their self-esteem until the end of life and what role key risk factors in the health, cognitive, self-regulatory, and social domains play. To examine these questions,…

US Urban Elementary Teachers' Knowledge and Practices in Teaching Science to English Language Learners: Results from the First Year of a Professional Development Intervention

ERIC Educational Resources Information Center

Santau, Alexandra O.; Secada, Walter; Maerten-Rivera, Jaime; Cone, Neporcha; Lee, Okhee

2010-01-01

The study examined US elementary teachers' knowledge and practices in four key domains of science instruction with English language learning (ELL) students. The four domains included: (1) teachers' knowledge of science content, (2) teaching practices to promote scientific understanding, (3) teaching practices to promote scientific inquiry, and (4)…

Effects of Military/Family Conflict on Female Naval Officer Retention

DTIC Science & Technology

2004-06-01

has the greatest impact on retention . Hierarchical regression was used to identify life domains (e.g., family factors, job experiences, job ...where work/family conflict has the greatest impact on retention . Hierarchical regression was used to identify life domains (e.g., family factors, job ...experiences, job satisfaction, and commitment) that are key drivers of retention intent among female Naval officers. By identifying areas that are

Impact of Trust on Security and Performance in Tactical Networks

DTIC Science & Technology

2013-06-01

and reliability . On the other hand, in organizational theory, trust management has viewed trust as a key factor to manage relationships that flourish...environments challenges, these dynamics can hinder accurate and reliable trust evaluation of entities in the network [10], [11]. • Information Network Domain...trustworthy entities. • Social/Cognitive Network Domain: Social scientists, physiologists, and neuroscientists have studied social trust, interpersonal

The Cyber War: Maintaining and Controlling the Key Cyber Terrain of the Cyberspace Domain

DTIC Science & Technology

2016-06-26

solution strategy to assess options that will enable the commander to realize the Air Force’s cyber mission. Recommendations will be made that will...will present a solution to assist the JFC in achieving cyberspace dominance. Background In the modern world of advanced technology, control of...the solutions are: 1) timely identification of key cyber terrain, 2) accurate mapping of the cyber terrain, 3) defense of key cyber terrain, and 4

Protein sorting by lipid phase-like domains supports emergent signaling function in B lymphocyte plasma membranes.

PubMed

Stone, Matthew B; Shelby, Sarah A; Núñez, Marcos F; Wisser, Kathleen; Veatch, Sarah L

2017-02-01

Diverse cellular signaling events, including B cell receptor (BCR) activation, are hypothesized to be facilitated by domains enriched in specific plasma membrane lipids and proteins that resemble liquid-ordered phase-separated domains in model membranes. This concept remains controversial and lacks direct experimental support in intact cells. Here, we visualize ordered and disordered domains in mouse B lymphoma cell membranes using super-resolution fluorescence localization microscopy, demonstrate that clustered BCR resides within ordered phase-like domains capable of sorting key regulators of BCR activation, and present a minimal, predictive model where clustering receptors leads to their collective activation by stabilizing an extended ordered domain. These results provide evidence for the role of membrane domains in BCR signaling and a plausible mechanism of BCR activation via receptor clustering that could be generalized to other signaling pathways. Overall, these studies demonstrate that lipid mediated forces can bias biochemical networks in ways that broadly impact signal transduction.

Nonlinear (time domain) and linearized (time and frequency domain) solutions to the compressible Euler equations in conservation law form

NASA Technical Reports Server (NTRS)

Sreenivas, Kidambi; Whitfield, David L.

1995-01-01

Two linearized solvers (time and frequency domain) based on a high resolution numerical scheme are presented. The basic approach is to linearize the flux vector by expressing it as a sum of a mean and a perturbation. This allows the governing equations to be maintained in conservation law form. A key difference between the time and frequency domain computations is that the frequency domain computations require only one grid block irrespective of the interblade phase angle for which the flow is being computed. As a result of this and due to the fact that the governing equations for this case are steady, frequency domain computations are substantially faster than the corresponding time domain computations. The linearized equations are used to compute flows in turbomachinery blade rows (cascades) arising due to blade vibrations. Numerical solutions are compared to linear theory (where available) and to numerical solutions of the nonlinear Euler equations.

Building a road map for tailoring multilayer polyelectrolyte films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ankner, John Francis; Bardoel, Agatha A; Sukishvili, Svetlana

2012-01-01

Researchers are moving a step closer to a definite road map for building layer-by-layer (LbL) assembled polyelectrolyte films, with the assistance of the Liquids Reflectometer at Oak Ridge National Laboratory's Spallation Neutron Source, in Oak Ridge, Tennessee. Scientists using the liquids reflectometer have successfully taken snapshots in close to real time of these multilayered structures for different applications when they modify the structure and function parameters. Polyelecrolytes are polymers that carry charge in aqueous solutions. They contain chemical groups that dissociate in water, making such polymers charged. Most polyelectrolytes are water soluble. They are important components in foods, soaps, shampoos,more » and cosmetics products. They show promise for such environmental work as oil recovery and water treatment. Polyelectrolytes are compelling because researchers can chemically modify how they interact with water for multiple applications. When two types of polyelectrolytes of opposite charge are assembled at a surface in a sequential way using the LbL assembly technique, 'the result is the forming of surface films, useful for coatings, biomedical implants and devices, controlling adhesion of biological molecules, and controlling delivery of therapeutic molecules from surfaces,' said Svetlana Sukhishvili of the Stevens Institute of Technology in New Jersey, the lead chemist on the collaboration. 'Medical doctors often prefer to deliver multiple therapeutic compounds from the coatings in a time-resolved manner,' Sukhishvili said. 'To assist them, material scientists need to learn how to build coatings in which polymer layering will not be compromised when exposed to normal physiological conditions.' 'Being able to control these properties, understanding how what you do to the materials affects their properties, this allows you to apply them to situations where interacting with an environment is very helpful, whether in a biological context or any other kind of water soluble context,' said John Ankner, lead instrument scientist for the Liquids Reflectometer. Ankner said that when several parameters are systematically altered, that allows researchers to map out the whole range of structures in the polymer. 'This work really sets a road map for how to get started with synthesizing polyelectrolyte materials for specific applications. Then, one can say, ok, this methylated material, the one that is 30% charged, is going to be what we want to use for a particular application.' The ORNL collaboration with the Stevens Institute has been conducting a series of experiments at the SNS to study layered film stratification in these polymers. Researchers stitch the polyelectrolyte chains in the LbL films together through what is called ionic pairing and arrange them within fuzzy, ultrathin layers that lie parallel to a solid surface substrate. Exposure of these films to aqueous solutions that contain salt (i.e., conditions that imitate real life) can compromise this film layering, as the salt ions act to weaken the ionic pairing that binds such layers together. So salt solutions are of key interest in studying how to make such layers for use in human applications. In the first research, Ankner, Sukhishvili and her student Li Xu looked at the effects of the layering of two types of LbL films of changing the charge density with a salt solution, and of blocking access to a charged site by nearby groups. The films were composed of positively charged variants of PDMA, a methyl polymer, and PDEA, an ethyl polymer. The other component of both systems is the ion exchanger polystyrene sulfonate (PSS) which features a fixed negative charge. First, a silicon substrate was dipped into solutions of PDMA and PDEA in dilute sodium chloride for a fixed time. Depending on the deposition time and the concentration of the solution, a nanometer-thick monolayer of the polymer adsorbs to the silicon surface. The film buildup is then continued by depositing a layer of PSS, and the cycle is repeated. The PDMA (methyl)/PSS and PDEA (ethyl)/PSS films were then annealed in varying concentrations of aqueous salt solutions. The chemists wanted to know if in these multi-layer cake-like assemblies, the structure can be systematically altered by varying the salt concentration, time in solution, and ultimately other environmental parameters, such as temperature or pH. Neutron reflectivity of the layered films exhibits the quality of the layering, in particular the concentration of the layers and how intermixed they are with adjacent layers. In this research, neutron reflectivity data from films built from 10%, 40%, and 100% charged PDMA or PDEA polyelectrolytes and 100% charged PSS were quantitatively compared to predicted, layered arrangements until the models produced reflectivity patterns matching those of the data.« less

Effective Schooling in Rural Africa Report 2: Key Issues Concerning School Effectiveness and Improvement.

ERIC Educational Resources Information Center

Saunders, Lesley

This report presents an overview of the literature on school/teacher effectiveness and improvement, with a focus on implications for developing countries. Sections 1-2 discuss the trend toward site-based management, which has increased pressures on individual schools and their staff; eight key domains of school effectiveness; and the need to…

Operational Details of the Five Domains Model and Its Key Applications to the Assessment and Management of Animal Welfare

PubMed Central

Mellor, David J.

2017-01-01

Simple Summary The Five Domains Model is a focusing device to facilitate systematic, structured, comprehensive and coherent assessment of animal welfare; it is not a definition of animal welfare, nor is it intended to be an accurate representation of body structure and function. The purpose of each of the five domains is to draw attention to areas that are relevant to both animal welfare assessment and management. This paper begins by briefly describing the major features of the Model and the operational interactions between the five domains, and then it details seven interacting applications of the Model. These underlie its utility and increasing application to welfare assessment and management in diverse animal use sectors. Abstract In accord with contemporary animal welfare science understanding, the Five Domains Model has a significant focus on subjective experiences, known as affects, which collectively contribute to an animal’s overall welfare state. Operationally, the focus of the Model is on the presence or absence of various internal physical/functional states and external circumstances that give rise to welfare-relevant negative and/or positive mental experiences, i.e., affects. The internal states and external circumstances of animals are evaluated systematically by referring to each of the first four domains of the Model, designated “Nutrition”, “Environment”, “Health” and “Behaviour”. Then affects, considered carefully and cautiously to be generated by factors in these domains, are accumulated into the fifth domain, designated “Mental State”. The scientific foundations of this operational procedure, published in detail elsewhere, are described briefly here, and then seven key ways the Model may be applied to the assessment and management of animal welfare are considered. These applications have the following beneficial objectives—they (1) specify key general foci for animal welfare management; (2) highlight the foundations of specific welfare management objectives; (3) identify previously unrecognised features of poor and good welfare; (4) enable monitoring of responses to specific welfare-focused remedial interventions and/or maintenance activities; (5) facilitate qualitative grading of particular features of welfare compromise and/or enhancement; (6) enable both prospective and retrospective animal welfare assessments to be conducted; and, (7) provide adjunct information to support consideration of quality of life evaluations in the context of end-of-life decisions. However, also noted is the importance of not overstating what utilisation of the Model can achieve. PMID:28792485

Identification of novel key amino acids at the interface of the transmembrane domains of human BST-2 and HIV-1 Vpu.

PubMed

Pang, Xiaojing; Hu, Siqi; Li, Jian; Xu, Fengwen; Mei, Shan; Zhou, Jinming; Cen, Shan; Jin, Qi; Guo, Fei

2013-08-06

BST-2 (bone marrow stromal cell antigen 2) is an interferon-inducible protein that inhibits virus release by tethering viral particles to the cell surface. This antiviral activity of BST-2 is antagonized by HIV-1 accessory protein Vpu. Vpu physically interacts with BST-2 through their mutual transmembrane (TM) domains. In this study, we utilized the BRET assay and molecular dynamics (MD) simulation method to further characterize the interaction of BST-2 and Vpu. Amino acids I34, L37, P40 and L41 in the TM domain of BST-2, and L11, A18 and W22 in the TM domain of Vpu were identified to be critical for the interaction between BST-2 and Vpu. The residues P40 in the TM domain of BST-2 and L11 in the TM domain of Vpu were shown, for the first time, to be important for their interaction. Furthermore, triple-amino-acid substitutions, 14-16 (AII to VAA) and 26-28 (IIE to AAA) in Vpu TM, not the single-residue mutation, profoundly disrupted BST-2/Vpu interaction. The results of MD simulation revealed significant conformational changes of the BST-2/Vpu complex as a result of mutating P40 of BST-2 and L11, 14-16 (AII to VAA) and 26-28 (IIE to AAA) of Vpu. In addition, disrupting the interaction between BST-2 and Vpu rendered BST-2 resistant to Vpu antagonization. Through use of the BRET assay, we identified novel key residues P40 in the TM domain of BST-2 and L11 in the TM domain of Vpu that are important for their interaction. These results add new insights into the molecular mechanism behind BST-2 antagonization by HIV-1 Vpu.

Identification of novel key amino acids at the interface of the transmembrane domains of human BST-2 and HIV-1 Vpu

PubMed Central

2013-01-01

Background BST-2 (bone marrow stromal cell antigen 2) is an interferon-inducible protein that inhibits virus release by tethering viral particles to the cell surface. This antiviral activity of BST-2 is antagonized by HIV-1 accessory protein Vpu. Vpu physically interacts with BST-2 through their mutual transmembrane (TM) domains. In this study, we utilized the BRET assay and molecular dynamics (MD) simulation method to further characterize the interaction of BST-2 and Vpu. Results Amino acids I34, L37, P40 and L41 in the TM domain of BST-2, and L11, A18 and W22 in the TM domain of Vpu were identified to be critical for the interaction between BST-2 and Vpu. The residues P40 in the TM domain of BST-2 and L11 in the TM domain of Vpu were shown, for the first time, to be important for their interaction. Furthermore, triple-amino-acid substitutions, 14–16 (AII to VAA) and 26–28 (IIE to AAA) in Vpu TM, not the single-residue mutation, profoundly disrupted BST-2/Vpu interaction. The results of MD simulation revealed significant conformational changes of the BST-2/Vpu complex as a result of mutating P40 of BST-2 and L11, 14–16 (AII to VAA) and 26–28 (IIE to AAA) of Vpu. In addition, disrupting the interaction between BST-2 and Vpu rendered BST-2 resistant to Vpu antagonization. Conclusions Through use of the BRET assay, we identified novel key residues P40 in the TM domain of BST-2 and L11 in the TM domain of Vpu that are important for their interaction. These results add new insights into the molecular mechanism behind BST-2 antagonization by HIV-1 Vpu. PMID:23919512

EssC: domain structures inform on the elusive translocation channel in the Type VII secretion system

PubMed Central

Zoltner, Martin; Ng, Wui M.A.V.; Money, Jillian J.; Fyfe, Paul K.; Kneuper, Holger; Palmer, Tracy; Hunter, William N.

2016-01-01

The membrane-bound protein EssC is an integral component of the bacterial Type VII secretion system (T7SS), which is a determinant of virulence in important Gram-positive pathogens. The protein is predicted to consist of an intracellular repeat of forkhead-associated (FHA) domains at the N-terminus, two transmembrane helices and three P-loop-containing ATPase-type domains, D1–D3, forming the C-terminal intracellular segment. We present crystal structures of the N-terminal FHA domains (EssC-N) and a C-terminal fragment EssC-C from Geobacillus thermodenitrificans, encompassing two of the ATPase-type modules, D2 and D3. Module D2 binds ATP with high affinity whereas D3 does not. The EssC-N and EssC-C constructs are monomeric in solution, but the full-length recombinant protein, with a molecular mass of approximately 169 kDa, forms a multimer of approximately 1 MDa. The observation of protomer contacts in the crystal structure of EssC-C together with similarity to the DNA translocase FtsK, suggests a model for a hexameric EssC assembly. Such an observation potentially identifies the key, and to date elusive, component of pore formation required for secretion by this recently discovered secretion system. The juxtaposition of the FHA domains suggests potential for interacting with other components of the secretion system. The structural data were used to guide an analysis of which domains are required for the T7SS machine to function in pathogenic Staphylococcus aureus. The extreme C-terminal ATPase domain appears to be essential for EssC activity as a key part of the T7SS, whereas D2 and FHA domains are required for the production of a stable and functional protein. PMID:27130157

An EarthCube Roadmap for Cross-Domain Interoperability in the Geosciences: Governance Aspects

NASA Astrophysics Data System (ADS)

Zaslavsky, I.; Couch, A.; Richard, S. M.; Valentine, D. W.; Stocks, K.; Murphy, P.; Lehnert, K. A.

2012-12-01

The goal of cross-domain interoperability is to enable reuse of data and models outside the original context in which these data and models are collected and used and to facilitate analysis and modeling of physical processes that are not confined to disciplinary or jurisdictional boundaries. A new research initiative of the U.S. National Science Foundation, called EarthCube, is developing a roadmap to address challenges of interoperability in the earth sciences and create a blueprint for community-guided cyberinfrastructure accessible to a broad range of geoscience researchers and students. Infrastructure readiness for cross-domain interoperability encompasses the capabilities that need to be in place for such secondary or derivative-use of information to be both scientifically sound and technically feasible. In this initial assessment we consider the following four basic infrastructure components that need to be present to enable cross-domain interoperability in the geosciences: metadata catalogs (at the appropriate community defined granularity) that provide standard discovery services over datasets, data access services, models and other resources of the domain; vocabularies that support unambiguous interpretation of domain resources and metadata; services used to access data repositories and other resources including models, visualizations and workflows; and formal information models that define structure and semantics of the information returned on service requests. General standards for these components have been proposed; they form the backbone of large scale integration activities in the geosciences. By utilizing these standards, EarthCube research designs can take advantage of data discovery across disciplines using the commonality in key data characteristics related to shared models of spatial features, time measurements, and observations. Data can be discovered via federated catalogs and linked nomenclatures from neighboring domains, while standard data services can be used to transparently compile composite data products. Key questions addressed in this presentation are: (1) How to define and assess readiness of existing domain information systems for cross-domain re-use? (2) How to determine EarthCube development priorities given a multitude of use cases that involve cross-domain data flows? and (3) How to involve a wider community of geoscientists in the development and curation of cross-domain resources and incorporate community feedback in the CI design? Answering them involves consideration of governance mechanisms for cross-domain interoperability: while domain information systems and projects developed governance mechanisms, managing cross-domain CI resources and supporting cross-domain information re-use hasn't been the development focus at the scale of the geosciences. We present a cross-domain readiness model as enabling effective communication among scientists, governance bodies, and information providers. We also present an initial readiness assessment and a cross-domain connectivity map for the geosciences, and outline processes for eliciting user requirements, setting priorities, and obtaining community consensus.

Crystal Structure of the Neuropilin-1 MAM Domain: Completing the Neuropilin-1 Ectodomain Picture.

PubMed

Yelland, Tamas; Djordjevic, Snezana

2016-11-01

Neuropilins (NRPs) are single-pass transmembrane receptors involved in several signaling pathways that regulate key physiological processes such as vascular morphogenesis and axon guidance. The MAM domain of NRP, which has previously been implicated in receptor multimerization, was the only portion of the ectopic domain of the NRPs for which the structure, until now, has been elusive. Using site-directed mutagenesis in the linker region preceding the MAM domain we generated a protein construct amenable to crystallization. Here we present the crystal structure of the MAM domain of human NRP1 at 2.24 Å resolution. The protein exhibits a jellyroll topology, with Ca 2+ ions bound at the inter-strand space enhancing the thermostability of the domain. We show that the MAM domain of NRP1 is monomeric in solution and insufficient to drive receptor dimerization, which leads us to propose a different role for this domain in the context of NRP membrane assembly and signaling. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Magnetic Fields of Lunar Impact Basins and Their Use in Constraining the Impact Process

NASA Astrophysics Data System (ADS)

Halekas, J. S.; Lin, R. P.

2003-01-01

Measurements by the Magnetometer/Electron Reflectometer instrument on the Lunar Prospector spacecraft, which completed its mapping mission in 1999, have been used to construct the first completely global maps of lunar crustal magnetic fields. Now, for the first time, we have a data set with global coverage and a sensitivity and resolution which allow us to investigate the magnetic fields of lunar impact basins and craters. As on the Earth, impact sites have a variety of magnetic signatures associated with them, ranging from nearly complete demagnetization to strong central magnetic anomalies. Observations of the magnetic fields of terrestrial basins have been used to make inferences about the impact process, and we wish to show that lunar observations can also provide valuable constraints.

Experiment and application of soft x-ray grazing incidence optical scattering phenomena

NASA Astrophysics Data System (ADS)

Chen, Shuyan; Li, Cheng; Zhang, Yang; Su, Liping; Geng, Tao; Li, Kun

2017-08-01

For short wavelength imaging systems，surface scattering effects is one of important factors degrading imaging performance. Study of non-intuitive surface scatter effects resulting from practical optical fabrication tolerances is a necessary work for optical performance evaluation of high resolution short wavelength imaging systems. In this paper, Soft X-ray optical scattering distribution is measured by a soft X-ray reflectometer installed by my lab, for different sample mirrors、wavelength and grazing angle. Then aim at space solar telescope, combining these scattered light distributions, and surface scattering numerical model of grazing incidence imaging system, PSF and encircled energy of optical system of space solar telescope are computed. We can conclude that surface scattering severely degrade imaging performance of grazing incidence systems through analysis and computation.

Development of a polarized neutron beam line at Algerian research reactors using McStas software

NASA Astrophysics Data System (ADS)

Makhloufi, M.; Salah, H.

2017-02-01

Unpolarized instrumentation has long been studied and designed using McStas simulation tool. But, only recently new models were developed for McStas to simulate polarized neutron scattering instruments. In the present contribution, we used McStas software to design a polarized neutron beam line, taking advantage of the available spectrometers reflectometer and diffractometer in Algeria. Both thermal and cold neutron was considered. The polarization was made by two types of supermirrors polarizers FeSi and CoCu provided by the HZB institute. For sake of performance and comparison, the polarizers were characterized and their characteristics reproduced. The simulated instruments are reported. Flipper and electromagnets for guide field are developed. Further developments including analyzers and upgrading of the existing spectrometers are underway.

'That's not masculine': masculine capital and health-related behaviour.

PubMed

De Visser, Richard O; Smith, Jonathan A; McDonnell, Elizabeth J

2009-10-01

In recent years increasing attention has been given to how different masculinities are expressed in young men's health behaviour. To examine whether men can use competence in key health-related masculine domains to compensate for other non-masculine behaviour, group discussions were conducted with men aged 18-21 living in London, England. The analysis revealed the ways in which competence in traditionally masculine health-related domains produces masculine 'capital', which can be used to compensate for non-masculine behaviour in other domains. However, the capacity to trade this capital is limited because different masculine and non-masculine behaviours have different values.

Curricular Approaches in Research Ethics Education: Reflecting on More and Less Effective Practices in Instructional Content.

PubMed

Torrence, Brett S; Watts, Logan L; Mulhearn, Tyler J; Turner, Megan R; Todd, E Michelle; Mumford, Michael D; Connelly, Shane

2017-01-01

Over the past decade, the effectiveness of ethics education programs has increased with regard to trainee outcomes, such as knowledge, awareness, and ethical decision making. However, despite the overall improvement in training effectiveness, considerable variability still exists across programs. One potential source of variability arises from the substantial range in instructional training content utilized across ethics training courses. The goal of the present effort was to clarify which approaches in ethics education result in positive training outcomes through the identification of instructional content themes. Through a qualitative review of ethics training courses, we identified key themes in instructional content curriculum associated with effective courses: domain-general, domain-specific, standard compliance, professionalism, and process-based. In addition, we identified key themes associated with less effective courses: mixed-specificity, narrow coverage, and idealized ethics. Descriptions and key characteristics of each theme along with example courses are provided. Implications of the content themes for ethics education are discussed.

A Study of the Shaping of the "Emotion and Attitude" Domain in the New English Language Curriculum of China through an EFL Textbook

ERIC Educational Resources Information Center

Ma, A.

2012-01-01

The English language curriculum (ELC) in China has undergone numerous changes since its modernisation movement in the late 1970s. The recent English language syllabus (2001) marks a new direction by incorporating "emotion and attitude" as one of the ELC's key domains. The implication is that the deep-rooted principle of learning a…

Relational Aggression, Victimization and Self-Concept: Testing Pathways from Middle Childhood to Adolescence.

PubMed

Blakely-McClure, Sarah J; Ostrov, Jamie M

2016-02-01

When studying adolescent development, it is important to consider two key areas that are salient for teens, which are self-concept and peer relations. A secondary analysis of the National Institute of Health and Human Development Study of Early Child Care and Youth Development was conducted to examine the prospective bidirectional associations between self-concept and peer relations. To date, how social development broadly and peer relations in particular (e.g., relational aggression and victimization) affect self-concept domains is not fully understood. Using a large sample (N = 1063; 532 girls; M = 11.14 years; SD = .59) with multiple informants, the present study examined whether fifth grade relational aggression and sixth grade relational victimization was associated with adolescent self-concept in three key domains (i.e., academic, sports, physical appearance). A significant direct effect emerged, such that relational aggression in middle childhood was associated with decreases in academic self-concept and increases in sports self-concept in adolescence. Analyses also revealed that having higher levels of domain specific self-concept led to decreases in relational aggression across the transition to adolescence. The findings highlight the importance of examining bidirectional prospective associations between relational aggression, relational victimization, and domain specific self-concept. Implications for future research and clinical intervention are discussed.

Time Domains of the Hypoxic Ventilatory Response and Their Molecular Basis

PubMed Central

Pamenter, Matthew E.; Powell, Frank L.

2016-01-01

Ventilatory responses to hypoxia vary widely depending on the pattern and length of hypoxic exposure. Acute, prolonged, or intermittent hypoxic episodes can increase or decrease breathing for seconds to years, both during the hypoxic stimulus, and also after its removal. These myriad effects are the result of a complicated web of molecular interactions that underlie plasticity in the respiratory control reflex circuits and ultimately control the physiology of breathing in hypoxia. Since the time domains of the physiological hypoxic ventilatory response (HVR) were identified, considerable research effort has gone toward elucidating the underlying molecular mechanisms that mediate these varied responses. This research has begun to describe complicated and plastic interactions in the relay circuits between the peripheral chemoreceptors and the ventilatory control circuits within the central nervous system. Intriguingly, many of these molecular pathways seem to share key components between the different time domains, suggesting that varied physiological HVRs are the result of specific modifications to overlapping pathways. This review highlights what has been discovered regarding the cell and molecular level control of the time domains of the HVR, and highlights key areas where further research is required. Understanding the molecular control of ventilation in hypoxia has important implications for basic physiology and is emerging as an important component of several clinical fields. PMID:27347896

Bandwidth and Fidelity on the NEO-Five Factor Inventory: Replicability and Reliability of Saucier’s (1998) Item Cluster Subcomponents

PubMed Central

Chapman, Benjamin P.

2012-01-01

Many users of the NEO-Five Factor Inventory (NEO-FFI; Costa & McCrae, 1992) are unaware that Saucier (1998) developed item cluster subcomponents for each broad domain of the instrument similar to the facets of the Revised NEO Personality Inventory (Costa & McCrae, 1992). In this study, I examined the following: the replicability of the subcomponents in young adult university and middle-aged community samples; whether item keying accounted for additional covariance among items; subcomponent correlations with a measure of socially desirable responding; subcomponent reliabilities; and subcomponent discriminant validity with respect to age-relevant criterion items expected to reflect varying associations with broad and narrow traits. Confirmatory factor analyses revealed that all subcomponents were recoverable across samples and that the addition of method factors representing positive and negative item keying improved model fit. The subcomponents correlated no more with a measure of socially desirable responding than their parent domains and showed good average reliability. Correlations with criterion items suggested that subcomponents may prove useful in specifying which elements of NEO-FFI domains are more or less related to variables of interest. I discuss their use for enhancing the precision of findings obtained with NEO-FFI domain scores. PMID:17437386

Imaging workflow and calibration for CT-guided time-domain fluorescence tomography

PubMed Central

Tichauer, Kenneth M.; Holt, Robert W.; El-Ghussein, Fadi; Zhu, Qun; Dehghani, Hamid; Leblond, Frederic; Pogue, Brian W.

2011-01-01

In this study, several key optimization steps are outlined for a non-contact, time-correlated single photon counting small animal optical tomography system, using simultaneous collection of both fluorescence and transmittance data. The system is presented for time-domain image reconstruction in vivo, illustrating the sensitivity from single photon counting and the calibration steps needed to accurately process the data. In particular, laser time- and amplitude-referencing, detector and filter calibrations, and collection of a suitable instrument response function are all presented in the context of time-domain fluorescence tomography and a fully automated workflow is described. Preliminary phantom time-domain reconstructed images demonstrate the fidelity of the workflow for fluorescence tomography based on signal from multiple time gates. PMID:22076264

Magnetic domain wall engineering in a nanoscale permalloy junction

NASA Astrophysics Data System (ADS)

Wang, Junlin; Zhang, Xichao; Lu, Xianyang; Zhang, Jason; Yan, Yu; Ling, Hua; Wu, Jing; Zhou, Yan; Xu, Yongbing

2017-08-01

Nanoscale magnetic junctions provide a useful approach to act as building blocks for magnetoresistive random access memories (MRAM), where one of the key issues is to control the magnetic domain configuration. Here, we study the domain structure and the magnetic switching in the Permalloy (Fe20Ni80) nanoscale magnetic junctions with different thicknesses by using micromagnetic simulations. It is found that both the 90-° and 45-° domain walls can be formed between the junctions and the wire arms depending on the thickness of the device. The magnetic switching fields show distinct thickness dependencies with a broad peak varying from 7 nm to 22 nm depending on the junction sizes, and the large magnetic switching fields favor the stability of the MRAM operation.

Chemical shift assignments of the partially deuterated Fyn SH2-SH3 domain.

PubMed

Kieken, Fabien; Loth, Karine; van Nuland, Nico; Tompa, Peter; Lenaerts, Tom

2018-04-01

Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1 H, 15 N and 13 C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.

Impact of protein domains on PE_PGRS30 polar localization in Mycobacteria.

PubMed

De Maio, Flavio; Maulucci, Giuseppe; Minerva, Mariachiara; Anoosheh, Saber; Palucci, Ivana; Iantomasi, Raffaella; Palmieri, Valentina; Camassa, Serena; Sali, Michela; Sanguinetti, Maurizio; Bitter, Wilbert; Manganelli, Riccardo; De Spirito, Marco; Delogu, Giovanni

2014-01-01

PE_PGRS proteins are unique to the Mycobacterium tuberculosis complex and a number of other pathogenic mycobacteria. PE_PGRS30, which is required for the full virulence of M. tuberculosis (Mtb), has three main domains, i.e. an N-terminal PE domain, repetitive PGRS domain and the unique C-terminal domain. To investigate the role of these domains, we expressed a GFP-tagged PE_PGRS30 protein and a series of its functional deletion mutants in different mycobacterial species (Mtb, Mycobacterium bovis BCG and Mycobacterium smegmatis) and analysed protein localization by confocal microscopy. We show that PE_PGRS30 localizes at the mycobacterial cell poles in Mtb and M. bovis BCG but not in M. smegmatis and that the PGRS domain of the protein strongly contributes to protein cellular localization in Mtb. Immunofluorescence studies further showed that the unique C-terminal domain of PE_PGRS30 is not available on the surface, except when the PGRS domain is missing. Immunoblot demonstrated that the PGRS domain is required to maintain the protein strongly associated with the non-soluble cellular fraction. These results suggest that the repetitive GGA-GGN repeats of the PGRS domain contain specific sequences that contribute to protein cellular localization and that polar localization might be a key step in the PE_PGRS30-dependent virulence mechanism.

Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.

PubMed

Kersting, Anna R; Mizrachi, Eshchar; Bornberg-Bauer, Erich; Myburg, Alexander A

2015-06-01

Eucalyptus is a pivotal genus within the rosid order Myrtales with distinct geographic history and adaptations. Comparative analysis of protein domain evolution in the newly sequenced Eucalyptus grandis genome and other rosid lineages sheds light on the adaptive mechanisms integral to the success of this genus of woody perennials. We reconstructed the ancestral domain content to elucidate the gain, loss and expansion of protein domains and domain arrangements in Eucalyptus in the context of rosid phylogeny. We used functional gene ontology (GO) annotation of genes to investigate the possible biological and evolutionary consequences of protein domain expansion. We found that protein modulation within the angiosperms occurred primarily on the level of expansion of certain domains and arrangements. Using RNA-Seq data from E. grandis, we showed that domain expansions have contributed to tissue-specific expression of tandemly duplicated genes. Our results indicate that tandem duplication of genes, a key feature of the Eucalyptus genome, has played an important role in the expansion of domains, particularly in proteins related to the specialization of reproduction and biotic and abiotic interactions affecting root and floral biology, and that tissue-specific expression of proteins with expanded domains has facilitated subfunctionalization in domain families. © 2014 University of Pretoria New Phytologist © 2014 New Phytologist Trust.

The Toxoplasma gondii cyst wall protein CST1 is critical for cyst wall integrity and promotes bradyzoite persistence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomita, Tadakimi; Bzik, David J.; Ma, Yan Fen

2013-12-26

Toxoplasma gondii infects up to one third of the world’s population. A key to the success of T.gondii is its ability to persist for the life of its host as bradyzoites within tissue cysts. The glycosylated cyst wall is the key structural feature that facilitates persistence and oral transmission of this parasite. We have identified CST1 (TGME49_064660) as a 250 kDa SRS (SAG1 related sequence) domain protein with a large mucin-like domain. CST1 is responsible for the Dolichos biflorus Agglutinin (DBA) lectin binding characteristic of T. gondii cysts. Deletion of CST1 results in a fragile brain cyst phenotype revealed bymore » a thinning and disruption of the underlying region of the cyst wall. These defects are reversed by complementation of CST1. Additional complementation experiments demonstrate that the CST1-mucin domain is necessary for the formation of a normal cyst wall structure, the ability of the cyst to resist mechanical stress and binding of DBA to the cyst wall. RNA-seq transcriptome analysis demonstrated dysregulation of bradyzoite genes within the various cst1 mutants. These results indicate that CST1 functions as a key structural component that reinforces the cyst wall structure and confers essential sturdiness to the T. gondii tissue cyst.« less

Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4.

PubMed

Sehar, Ujala; Mehmood, Muhammad Aamer; Hussain, Khadim; Nawaz, Salman; Nadeem, Shahid; Siddique, Muhammad Hussnain; Nadeem, Habibullah; Gull, Munazza; Ahmad, Niaz; Sohail, Iqra; Gill, Saba Shahid; Majeed, Summera

2013-01-01

This paper presents an in silico characterization of the chitin binding protein CBP50 from B. thuringiensis serovar konkukian S4 through homology modeling and molecular docking. The CBP50 has shown a modular structure containing an N-terminal CBM33 domain, two consecutive fibronectin-III (Fn-III) like domains and a C-terminal CBM5 domain. The protein presented a unique modular structure which could not be modeled using ordinary procedures. So, domain wise modeling using MODELLER and docking analyses using Autodock Vina were performed. The best conformation for each domain was selected using standard procedure. It was revealed that four amino acid residues Glu-71, Ser-74, Glu-76 and Gln-90 from N-terminal domain are involved in protein-substrate interaction. Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding. Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.

M-and-C Domain Map Maker: an environment complimenting MDE with M-and-C knowledge and ensuring solution completeness

NASA Astrophysics Data System (ADS)

Patwari, Puneet; Choudhury, Subhrojyoti R.; Banerjee, Amar; Swaminathan, N.; Pandey, Shreya

2016-07-01

Model Driven Engineering (MDE) as a key driver to reduce development cost of M&C systems is beginning to find acceptance across scientific instruments such as Radio Telescopes and Nuclear Reactors. Such projects are adopting it to reduce time to integrate, test and simulate their individual controllers and increase reusability and traceability in the process. The creation and maintenance of models is still a significant challenge to realizing MDE benefits. Creating domain-specific modelling environments reduces the barriers, and we have been working along these lines, creating a domain-specific language and environment based on an M&C knowledge model. However, large projects involve several such domains, and there is still a need to interconnect the domain models, in order to ensure modelling completeness. This paper presents a knowledge-centric approach to doing that, by creating a generic system model that underlies the individual domain knowledge models. We present our vision for M&C Domain Map Maker, a set of processes and tools that enables explication of domain knowledge in terms of domain models with mutual consistency relationships to aid MDE.

Characterizing Functional Domains for TIM-Mediated Enveloped Virus Entry

PubMed Central

Moller-Tank, Sven; Albritton, Lorraine M.; Rennert, Paul D.

2014-01-01

ABSTRACT T-cell immunoglobulin and mucin domain 1 (TIM-1) and other TIM family members were recently identified as phosphatidylserine (PtdSer)-mediated virus entry-enhancing receptors (PVEERs). These proteins enhance entry of Ebola virus (EBOV) and other viruses by binding PtdSer on the viral envelope, concentrating virus on the cell surface, and promoting subsequent internalization. The PtdSer-binding activity of the immunoglobulin-like variable (IgV) domain is essential for both virus binding and internalization by TIM-1. However, TIM-3, whose IgV domain also binds PtdSer, does not effectively enhance virus entry, indicating that other domains of TIM proteins are functionally important. Here, we investigate the domains supporting enhancement of enveloped virus entry, thereby defining the features necessary for a functional PVEER. Using a variety of chimeras and deletion mutants, we found that in addition to a functional PtdSer-binding domain PVEERs require a stalk domain of sufficient length, containing sequences that promote an extended structure. Neither the cytoplasmic nor the transmembrane domain of TIM-1 is essential for enhancing virus entry, provided the protein is still plasma membrane bound. Based on these defined characteristics, we generated a mimic lacking TIM sequences and composed of annexin V, the mucin-like domain of α-dystroglycan, and a glycophosphatidylinositol anchor that functioned as a PVEER to enhance transduction of virions displaying Ebola, Chikungunya, Ross River, or Sindbis virus glycoproteins. This identification of the key features necessary for PtdSer-mediated enhancement of virus entry provides a basis for more effective recognition of unknown PVEERs. IMPORTANCE T-cell immunoglobulin and mucin domain 1 (TIM-1) and other TIM family members are recently identified phosphatidylserine (PtdSer)-mediated virus entry-enhancing receptors (PVEERs). These proteins enhance virus entry by binding the phospholipid, PtdSer, present on the viral membrane. While it is known that the PtdSer binding is essential for the PVEER function of TIM-1, TIM-3 shares this binding activity but does not enhance virus entry. No comprehensive studies have been done to characterize the other domains of TIM-1. In this study, using a variety of chimeric proteins and deletion mutants, we define the features necessary for a functional PVEER. With these features in mind, we generated a TIM-1 mimic using functionally similar domains from other proteins. This mimic, like TIM-1, effectively enhanced transduction. These studies provide insight into the key features necessary for PVEERs and will allow for more effective identification of unknown PVEERs. PMID:24696470

Insight into structural rearrangements and interdomain interactions related to electron transfer between flavin mononucleotide and heme in nitric oxide synthase: A molecular dynamics study.

PubMed

Sheng, Yinghong; Zhong, Linghao; Guo, Dahai; Lau, Gavin; Feng, Changjian

2015-12-01

Calmodulin (CaM) binding to nitric oxide synthase (NOS) enables a conformational change, in which the FMN domain shuttles between the FAD and heme domains to deliver electrons to the active site heme center. A clear understanding of this large conformational change is critical, since this step is the rate-limiting in NOS catalysis. Herein molecular dynamics simulations were conducted on a model of an oxygenase/FMN (oxyFMN) construct of human inducible NOS (iNOS). This is to investigate the structural rearrangements and the domain interactions related to the FMN-heme interdomain electron transfer (IET). We carried out simulations on the iNOS oxyFMN·CaM complex models in [Fe(III)][FMNH(-)] and [Fe(II)][FMNH] oxidation states, the pre- and post-IET states. The comparison of the dynamics and conformations of the iNOS construct at the two oxidation states has allowed us to identify key factors related to facilitating the FMN-heme IET process. The computational results demonstrated, for the first time, that the conformational change is redox-dependent. Predictions of the key interacting sites in optimal interdomain FMN/heme docking are well supported by experimental data in the literature. An intra-subunit pivot region is predicted to modulate the FMN domain motion and correlate with existence of a bottleneck in the conformational sampling that leads to the electron transfer-competent state. Interactions of the residues identified in this work are proposed to ensure that the FMN domain moves with appropriate degrees of freedom and docks to proper positions at the heme domain, resulting in efficient IET and nitric oxide production. Copyright © 2015 Elsevier Inc. All rights reserved.

Data-driven Ontology Development: A Case Study at NASA's Atmospheric Science Data Center

NASA Astrophysics Data System (ADS)

Hertz, J.; Huffer, E.; Kusterer, J.

2012-12-01

Well-founded ontologies are key to enabling transformative semantic technologies and accelerating scientific research. One example is semantically enabled search and discovery, making scientific data accessible and more understandable by accurately modeling a complex domain. The ontology creation process remains a challenge for many anxious to pursue semantic technologies. The key may be that the creation process -- whether formal, community-based, automated or semi-automated -- should encompass not only a foundational core and supplemental resources but also a focus on the purpose or mission the ontology is created to support. Are there tools or processes to de-mystify, assess or enhance the resulting ontology? We suggest that comparison and analysis of a domain-focused ontology can be made using text engineering tools for information extraction, tokenizers, named entity transducers and others. The results are analyzed to ensure the ontology reflects the core purpose of the domain's mission and that the ontology integrates and describes the supporting data in the language of the domain - how the science is analyzed and discussed among all users of the data. Commonalities and relationships among domain resources describing the Clouds and Earth's Radiant Energy (CERES) Bi-Directional Scan (BDS) datasets from NASA's Atmospheric Science Data Center are compared. The domain resources include: a formal ontology created for CERES; scientific works such as papers, conference proceedings and notes; information extracted from the datasets (i.e., header metadata); and BDS scientific documentation (Algorithm Theoretical Basis Documents, collection guides, data quality summaries and others). These resources are analyzed using the open source software General Architecture for Text Engineering, a mature framework for computational tasks involving human language.

Structural modulation of factor VIIa by full-length tissue factor (TF1-263): implication of novel interactions between EGF2 domain and TF.

PubMed

Prasad, Ramesh; Sen, Prosenjit

2018-02-01

Tissue factor (TF)-mediated factor VII (FVII) activation and a subsequent proteolytic TF-FVIIa binary complex formation is the key step initiating the coagulation cascade, with implications in various homeostatic and pathologic scenarios. TF binding allosterically modifies zymogen-like free FVIIa to its highly catalytically active form. As a result of unresolved crystal structure of the full-length TF 1-263 -FVIIa binary complex and free FVIIa, allosteric alterations in FVIIa following its binding to full-length TF and the consequences of these on function are not entirely clear. The present study aims to map and identify structural alterations in FVIIa and TF resulting from full-length TF binding to FVIIa and the key events responsible for enhanced FVIIa activity in coagulation. We constructed the full-length TF 1-263 -FVIIa membrane bound complex using computational modeling and subjected it to molecular dynamics (MD) simulations. MD simulations showed that TF alters the structure of each domain of FVIIa and these combined alterations contribute to enhanced TF-FVIIa activity. Detailed, domain-wise investigation revealed several new non-covalent interactions between TF and FVIIa that were not found in the truncated soluble TF-FVIIa crystal structure. The structural modulation of each FVIIa domain imparted by TF indicated that both inter and intra-domain communication is crucial for allosteric modulation of FVIIa. Our results suggest that these newly formed interactions can provide additional stability to the protease domain and regulate its activity profile by governing catalytic triad (CT) orientation and localization. The unexplored newly formed interactions between EGF2 and TF provides a possible explanation for TF-induced allosteric activation of FVIIa.

Return-to-work activities in a Chinese cultural context.

PubMed

Cheng, Andy S K; Loisel, Patrick; Feuerstein, Michael

2011-03-01

Several studies have been conducted in the West showing that return to work (RTW) coordination is a key element to facilitate RTW of injured workers and to prevent work disabilities. However, no study has been carried out to investigate the scope of RTW activities in China. The purpose of this study was to explore the views of key RTW stakeholders on necessary activities for RTW coordination. A cross-sectional survey was conducted in Guangdong province of China. A three-tiered approach including focus group discussions and panel reviews was used to collect RTW activities, analyze the content validity, and classify domains. Descriptive statistics and intra-class correlation (ICC) were used to describe the importance of RTW activities and the degree of agreement on the classification of different domains. A Kruskal-Wallis test with subsequent post-hoc analysis using multiple Mann-Whitney U tests was carried out to check for any differences in the domains of different RTW activities among RTW stakeholders. The domains of RTW activities in China were similar to those in the West and included workplace assessment and mediation, social problem solving, role and liability clarification, and medical advice. Good agreement (ICC: 0.729-0.844) on the classification of RTW activities into different domains was found. The domains of the RTW activities of healthcare providers differed from those of employers (P = 0.002) and injured workers (P = 0.001). However, there was no significant difference between employers and injured workers. This study indicated that differences among stakeholders were observed in terms of areas of relative priority. There is a clear need for research and training in China to establish a nation-wide terminology for RTW coordination, facilitate cross-provincial studies and work toward a more integrated system addressing the diverse perspectives of stakeholders involved in the RTW process.

Homology modeling and in silico prediction of Ulcerative colitis associated polymorphisms of NOD1.

PubMed

Majumdar, Ishani; Nagpal, Isha; Paul, Jaishree

2017-10-01

Cytosolic pattern recognition receptors play key roles in innate immune response. Nucleotide binding and oligomerisation domain containing protein 1 (NOD1) belonging to the Nod-like receptor C (NLRC) sub-family of Nod-like receptors (NLRs) is important for detection and clearance of intra-cellular Gram negative bacteria. NOD1 is involved in activation of pro-inflammatory pathways. Limited structural data is available for NOD1. Using different templates for each domain of NOD1, we determined the full-length homology model of NOD1. ADP binding amino acids within the nucleotide binding domain (NBD) of NOD1 were also predicted. Key residues in inter-domain interaction were identified by sequence comparison with Oryctolagus cuniculus NOD2, a related protein. Interactions between NBD and winged helix domain (WHD) were found to be conserved in NOD1. Functional and structural effect of single nucleotide polymorphisms within the NOD1 NBD domain associated with susceptibility risk to Ulcerative colitis (UC), an inflammatory disorder of the colon was evaluated by in silico studies. Mutations W219R and L349P were predicted to be damaging and disease associated by prediction programs SIFT, PolyPhen2, PANTHER, SNP&GO, PhD SNP and SNAP2. We further validated the effect of W219R and L349P mutation on NOD1 function in vitro. Elevated mRNA expression of pro-inflammatory cytokines IL8 and IL-1β was seen as compared to the wild type NOD1 in intestinal epithelial cell line HT29 when stimulated with NOD1 ligand. Thus, these mutations may indeed have a bearing on pathogenesis of inflammation during UC. Copyright © 2017 Elsevier Ltd. All rights reserved.

Adoption and Design of Emerging Dietary Policies to Improve Cardiometabolic Health in the US.

PubMed

Huang, Yue; Pomeranz, Jennifer; Wilde, Parke; Capewell, Simon; Gaziano, Tom; O'Flaherty, Martin; Kersh, Rogan; Whitsel, Laurie; Mozaffarian, Dariush; Micha, Renata

2018-04-14

Suboptimal diet is a leading cause of cardiometabolic disease and economic burdens. Evidence-based dietary policies within 5 domains-food prices, reformulation, marketing, labeling, and government food assistance programs-appear promising at improving cardiometabolic health. Yet, the extent of new dietary policy adoption in the US and key elements crucial to define in designing such policies are not well established. We created an inventory of recent US dietary policy cases aiming to improve cardiometabolic health and assessed the extent of their proposal and adoption at federal, state, local, and tribal levels; and categorized and characterized the key elements in their policy design. Recent federal dietary policies adopted to improve cardiometabolic health include reformulation (trans-fat elimination), marketing (mass-media campaigns to increase fruits and vegetables), labeling (Nutrition Facts Panel updates, menu calorie labeling), and food assistance programs (financial incentives for fruits and vegetables in the Supplemental Nutrition Assistance Program (SNAP) and Women, Infant and Children (WIC) program). Federal voluntary guidelines have been proposed for sodium reformulation and food marketing to children. Recent state proposals included sugar-sweetened beverage (SSB) taxes, marketing restrictions, and SNAP restrictions, but few were enacted. Local efforts varied significantly, with certain localities consistently leading in the proposal or adoption of relevant policies. Across all jurisdictions, most commonly selected dietary targets included fruits and vegetables, SSBs, trans-fat, added sugar, sodium, and calories; other healthy (e.g., nuts) or unhealthy (e.g., processed meats) factors were largely not addressed. Key policy elements to define in designing these policies included those common across domains (e.g., level of government, target population, dietary target, dietary definition, implementation mechanism), and domain-specific (e.g., media channels for food marketing domain) or policy-specific (e.g., earmarking for taxes) elements. Characteristics of certain elements were similarly defined (e.g., fruit and vegetable definition, warning language used in SSB warning labels), while others varied across cases within a policy (e.g., tax base for SSB taxes). Several key elements were not always sufficiently characterized in government documents, and dietary target selections and definitions did not consistently align with the evidence-base. These findings highlight recent action on dietary policies to improve cardiometabolic health in the US; and key elements necessary to design such policies.

A new percolation model for composite solid electrolytes and dispersed ionic conductors

NASA Astrophysics Data System (ADS)

Risyad Hasyim, Muhammad; Lanagan, Michael T.

2018-02-01

Composite solid electrolytes (CSEs) including conductor/insulator composites known as dispersed ionic conductors (DICs) have motivated the development of novel percolation models that describe their conductivity. Despite the long history, existing models lack in one or more key areas: (1) rigorous foundation for their physical theory, (2) explanation for non-universal conductor-insulator transition, (3) classification of DICs, and (4) extension to frequency-domain. This work describes a frequency-domain effective medium approximation (EMA) of a bond percolation model for CSEs. The EMA is derived entirely from Maxwell’s equations and contains basic microstructure parameters. The model was applied successfully to several composite systems from literature. Simulations and fitting of literature data address these key areas and illustrate the interplay between space charge layer properties and bulk microstructure.

Analytic Steering: Inserting Context into the Information Dialog

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bohn, Shawn J.; Calapristi, Augustin J.; Brown, Shyretha D.

2011-10-23

An analyst’s intrinsic domain knowledge is a primary asset in almost any analysis task. Unstructured text analysis systems that apply un-supervised content analysis approaches can be more effective if they can leverage this domain knowledge in a manner that augments the information discovery process without obfuscating new or unexpected content. Current unsupervised approaches rely upon the prowess of the analyst to submit the right queries or observe generalized document and term relationships from ranked or visual results. We propose a new approach which allows the user to control or steer the analytic view within the unsupervised space. This process ismore » controlled through the data characterization process via user supplied context in the form of a collection of key terms. We show that steering with an appropriate choice of key terms can provide better relevance to the analytic domain and still enable the analyst to uncover un-expected relationships; this paper discusses cases where various analytic steering approaches can provide enhanced analysis results and cases where analytic steering can have a negative impact on the analysis process.« less

Antibody engineering reveals the important role of J segments in the production efficiency of llama single-domain antibodies in Saccharomyces cerevisiae.

PubMed

Gorlani, A; Hulsik, D Lutje; Adams, H; Vriend, G; Hermans, P; Verrips, T

2012-01-01

Variable domains of llama heavy-chain antibodies (VHH) are becoming a potent tool for a wide range of biotechnological and medical applications. Because of structural features typical of their single-domain nature, they are relatively easy to produce in lower eukaryotes, but it is not uncommon that some molecules have poor secretion efficiency. We therefore set out to study the production yield of VHH. We computationally identified five key residues that are crucial for folding and secretion, and we validated their importance with systematic site-directed mutations. The observation that all key residues were localised in the V segment, in proximity of the J segment of VHH, led us to study the importance of J segment in secretion efficiency. Intriguingly, we found that the use of specific J segments in VHH could strongly influence the production yield. Sequence analysis and expression experiments strongly suggested that interactions with chaperones, especially with the J segment, are a crucial aspect of the production yield of VHH.

Low performance on mathematical tasks in preschoolers: the importance of domain-general and domain-specific abilities.

PubMed

Costa, H M; Nicholson, B; Donlan, C; Van Herwegen, J

2018-04-01

Different domain-specific and domain-general cognitive precursors play a key role in the development of mathematical abilities. The contribution of these domains to mathematical ability changes during development. Primary school-aged children who show mathematical difficulties form a heterogeneous group, but it is not clear whether this also holds for preschool low achievers (LAs) and how domain-specific and domain-general abilities contribute to mathematical difficulties at a young age. The aim of this study was to explore the cognitive characteristics of a sample of preschool LAs and identify sub-types of LAs. 81 children were identified as LAs from 283 preschoolers aged 3 to 5 years old and were assessed on a number of domain-general and domain-specific tasks. Cluster analysis revealed four subgroups of LAs in mathematics: (1) a weak processing sub-type; (2) a general mathematical LAs sub-type; (3) a mixed abilities sub-type; and (4) a visuo-spatial deficit sub-type. Whilst two of the groups showed specific domain-general difficulties, none showed only domain-specific difficulties. Current findings suggest that preschool LAs constitute a heterogeneous group and stress the importance of domain-general factors for the development of mathematical abilities during the preschool years. © 2018 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Compact Conformations of Human Protein Disulfide Isomerase

PubMed Central

Cui, Lei; Ding, Xiang; Niu, Lili; Yang, Fuquan; Wang, Chao; Wang, Chih-chen; Lou, Jizhong

2014-01-01

Protein disulfide isomerase (PDI) composed of four thioredoxin-like domains a, b, b', and a', is a key enzyme catalyzing oxidative protein folding in the endoplasmic reticulum. Large scale molecular dynamics simulations starting from the crystal structures of human PDI (hPDI) in the oxidized and reduced states were performed. The results indicate that hPDI adopts more compact conformations in solution than in the crystal structures, which are stabilized primarily by inter-domain interactions, including the salt bridges between domains a and b' observed for the first time. A prominent feature of the compact conformations is that the two catalytic domains a and a' can locate close enough for intra-molecular electron transfer, which was confirmed by the characterization of an intermediate with a disulfide between the two domains. Mutations, which disrupt the inter-domain interactions, lead to decreased reductase activity of hPDI. Our molecular dynamics simulations and biochemical experiments reveal the intrinsic conformational dynamics of hPDI and its biological impact. PMID:25084354

Human Protein-disulfide Isomerase Is a Redox-regulated Chaperone Activated by Oxidation of Domain a′*

PubMed Central

Wang, Chao; Yu, Jiang; Huo, Lin; Wang, Lei; Feng, Wei; Wang, Chih-chen

2012-01-01

Protein-disulfide isomerase (PDI), with domains arranged as abb′xa′c, is a key enzyme and chaperone localized in the endoplasmic reticulum (ER) catalyzing oxidative folding and preventing misfolding/aggregation of proteins. It has been controversial whether the chaperone activity of PDI is redox-regulated, and the molecular basis is unclear. Here, we show that both the chaperone activity and the overall conformation of human PDI are redox-regulated. We further demonstrate that the conformational changes are triggered by the active site of domain a′, and the minimum redox-regulated cassette is located in b′xa′. The structure of the reduced bb′xa′ reveals for the first time that domain a′ packs tightly with both domain b′ and linker x to form one compact structural module. Oxidation of domain a′ releases the compact conformation and exposes the shielded hydrophobic areas to facilitate its high chaperone activity. Thus, the study unequivocally provides mechanistic insights into the redox-regulated chaperone activity of human PDI. PMID:22090031

A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies

PubMed Central

Zahn, Raphael; Osmanović, Dino; Ehret, Severin; Araya Callis, Carolina; Frey, Steffen; Stewart, Murray; You, Changjiang; Görlich, Dirk; Hoogenboom, Bart W; Richter, Ralf P

2016-01-01

The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior – a key element for the transport selectivity of the NPC – was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface. DOI: http://dx.doi.org/10.7554/eLife.14119.001 PMID:27058170

Time-domain damping models in structural acoustics using digital filtering

NASA Astrophysics Data System (ADS)

Parret-Fréaud, Augustin; Cotté, Benjamin; Chaigne, Antoine

2016-02-01

This paper describes a new approach in order to formulate well-posed time-domain damping models able to represent various frequency domain profiles of damping properties. The novelty of this approach is to represent the behavior law of a given material directly in a discrete-time framework as a digital filter, which is synthesized for each material from a discrete set of frequency-domain data such as complex modulus through an optimization process. A key point is the addition of specific constraints to this process in order to guarantee stability, causality and verification of thermodynamics second law when transposing the resulting discrete-time behavior law into the time domain. Thus, this method offers a framework which is particularly suitable for time-domain simulations in structural dynamics and acoustics for a wide range of materials (polymers, wood, foam, etc.), allowing to control and even reduce the distortion effects induced by time-discretization schemes on the frequency response of continuous-time behavior laws.

Tunable inertia of chiral magnetic domain walls

PubMed Central

Torrejon, Jacob; Martinez, Eduardo; Hayashi, Masamitsu

2016-01-01

The time it takes to accelerate an object from zero to a given velocity depends on the applied force and the environment. If the force ceases, it takes exactly the same time to completely decelerate. A magnetic domain wall is a topological object that has been observed to follow this behaviour. Here we show that acceleration and deceleration times of chiral Neel walls driven by current are different in a system with low damping and moderate Dzyaloshinskii–Moriya exchange constant. The time needed to accelerate a domain wall with current via the spin Hall torque is much faster than the time it needs to decelerate once the current is turned off. The deceleration time is defined by the Dzyaloshinskii–Moriya exchange constant whereas the acceleration time depends on the spin Hall torque, enabling tunable inertia of chiral domain walls. Such unique feature of chiral domain walls can be utilized to move and position domain walls with lower current, key to the development of storage class memory devices. PMID:27882932

Thrombospondin Type-1 Repeat Domain-Containing Proteins Are Strongly Expressed in the Head Region of Hydra.

PubMed

Hamaguchi-Hamada, Kayoko; Kurumata-Shigeto, Mami; Minobe, Sumiko; Fukuoka, Nozomi; Sato, Manami; Matsufuji, Miyuki; Koizumi, Osamu; Hamada, Shun

2016-01-01

The head region of Hydra, the hypostome, is a key body part for developmental control and the nervous system. We herein examined genes specifically expressed in the head region of Hydra oligactis using suppression subtractive hybridization (SSH) cloning. A total of 1414 subtracted clones were sequenced and found to be derived from at least 540 different genes by BLASTN analyses. Approximately 25% of the subtracted clones had sequences encoding thrombospondin type-1 repeat (TSR) domains, and were derived from 17 genes. We identified 11 TSR domain-containing genes among the top 36 genes that were the most frequently detected in our SSH library. Whole-mount in situ hybridization analyses confirmed that at least 13 out of 17 TSR domain-containing genes were expressed in the hypostome of Hydra oligactis. The prominent expression of TSR domain-containing genes suggests that these genes play significant roles in the hypostome of Hydra oligactis.

The Extracellular δ-Domain is Essential for the Formation of CD81 Tetraspanin Webs

PubMed Central

Homsi, Yahya; Schloetel, Jan-Gero; Scheffer, Konstanze D.; Schmidt, Thomas H.; Destainville, Nicolas; Florin, Luise; Lang, Thorsten

2014-01-01

CD81 is a ubiquitously expressed member of the tetraspanin family. It forms large molecular platforms, so-called tetraspanin webs that play physiological roles in a variety of cellular functions and are involved in viral and parasite infections. We have investigated which part of the CD81 molecule is required for the formation of domains in the cell membranes of T-cells and hepatocytes. Surprisingly, we find that large CD81 platforms assemble via the short extracellular δ-domain, independent from a strong primary partner binding and from weak interactions mediated by palmitoylation. The δ-domain is also essential for the platforms to function during viral entry. We propose that, instead of stable binary interactions, CD81 interactions via the small δ-domain, possibly involving a dimerization step, play the key role in organizing CD81 into large tetraspanin webs and controlling its function. PMID:24988345

Test and Evaluation of Fiber Optic Sensors for High-Radiation Space Nuclear Power Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klemer, Daniel; Fielder, Robert S.; Stinson-Bagby, Kelly L.

2004-07-01

Fiber optic sensors can be used to measure a number of parameters, including temperature, strain, pressure and flow, for instrumentation and control of space nuclear power systems. In the past, this technology has often been rejected for use in such a high-radiation environment based on early experiments that revealed a number of degradation phenomena, including radiation-induced fiber attenuation, or 'graying', and Fiber Bragg Grating (FBG) fading and wavelength shift. However, this paper reports the results of recent experimental testing that demonstrates readability of fiber optic sensors to extremely high levels of neutron and gamma radiation. Both distributed Fiber Bragg Gratingmore » (FBG) sensors and single-point Extrinsic Fabry Perot Interferometer (EFPI) sensors were continuously monitored over a 2-month period, during which they were exposed to combined neutron and gamma radiation in both in-core and ex-core positions within a nuclear reactor. Total exposure reached approximately 2 x 10{sup 19} cm{sup -2} fast neutron (E > 1 MeV) fluence and 8.7 x 10{sup 8} Gy gamma for in-core sensors. FBG sensors were interrogated using a standard Luna Innovations FBG measurement system, which is based on optical frequency-domain reflectometer (OFDR) technology. Approximately 74% of the 19 FBG sensors located at the core centerline in the in-core position exhibited sufficient signal-to-noise ratio (SNR) to remain readable even after receiving the maximum dose. EFPI sensors were spectrally interrogated using a broadband probe source operating in the 830 nm wavelength region. While these single-point sensors failed early in the test, important additional fiber spectral transmission data was collected, which indicates that interrogation of EFPI sensors in alternate wavelength regions may allow significant improvement in sensor longevity for operation in high-radiation environments. This work was funded through a Small Business Innovative Research (SBIR) contract with the Nasa Glenn Research Center. (authors)« less

Hydrological monitoring of a natural slope covered with loose granular pyroclastic deposits

NASA Astrophysics Data System (ADS)

Damiano, Emilia; Greco, Roberto; Guida, Andrea; Olivares, Lucio; Picarelli, Luciano

2010-05-01

Mountainous areas of Northern Campania, Southern Italy, are characterised by steep slopes covered with loose volcanic ashes, with very high porosity (ranging between 0.70 and 0.75), laying above a calcareous bedrock. Slope inclination is often larger than internal friction angle of such ashes (around 38°), thus equilibrium is assured by the contribution of apparent cohesion due to soil suction in unsaturated conditions. That is why, during intense and persistent rainfall events, when soil approaches saturation and consequently suction decreases, shallow landslides are frequently triggered. The physical characteristics of involved soils are such that landslides often evolve in form of debris flows, which cause huge damages to buildings and infrastructures and, in some cases, even casualties. Field hydrological monitoring is essential to develop reliable models of slope response to rainfall infiltration, allowing to define triggering conditions of landslides. An automatic monitoring station has been recently installed at the slope of Cervinara, 30 km East of Naples, where a catastrophic landslide occurred in December 1999. The station consists of a tipping bucket rain gauge, with a sensitivity to rainfall height of 0.2mm; four jet fill tensiometers, for the measurement of soil suction at the depths of 10cm, 40cm, 120cm and 160cm below ground surface; four time domain reflectometry probes of various lengths, connected through a multiplexer to a reflectometer, for the measurement of water content profile from ground surface up to a depth of 160cm. All the sensors are connected to a datalogger for the automatic acquisition at hourly frequency of experimental data. Acquired data are then stored into a magnetic memory which is periodically downloaded into a PC. The entire station is operated by a lithium battery connected to a solar panel. The first collected experimental data confirm the usefulness of simultaneous monitoring, at high temporal resolution, of rainfall height, soil suction and soil water content for a better understanding of slope infiltration processes.

Structural insights into the functional versatility of WW domain-containing oxidoreductase tumor suppressor

PubMed Central

2015-01-01

Recent work on WW domain-containing oxidoreductase (WWOX) tumor suppressor is beginning to shed new light on both the molecular mechanism of action of its WW domains as well as the contiguous catalytic domain. Herein, the structural basis underlying the ability of WW1 domain to bind to various physiological ligands and how the orphan WW2 tandem partner synergizes its ligand binding in the context of WW1–WW2 tandem module of WWOX is discussed. Notably, the WW domains within the WW1–WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. In this manner, the association of WW2 domain with WW1 hinders ligand binding to the latter. Consequently, ligand binding to WW1 domain not only results in the displacement of WW2 lid but also disrupts the fixed orientation of WW domains in the liganded conformation. Equally importantly, structure-guided functional approach suggests that the catalytic domain of WWOX likely serves as a retinal oxidoreductase that catalyzes the reversible oxidation and reduction of all-trans-retinal. Collectively, this review provides structural insights into the functional versatility of a key signaling protein with important implications on its biology. PMID:25662954

Structural insights into the functional versatility of WW domain-containing oxidoreductase tumor suppressor.

PubMed

Farooq, Amjad

2015-03-01

Recent work on WW domain-containing oxidoreductase (WWOX) tumor suppressor is beginning to shed new light on both the molecular mechanism of action of its WW domains as well as the contiguous catalytic domain. Herein, the structural basis underlying the ability of WW1 domain to bind to various physiological ligands and how the orphan WW2 tandem partner synergizes its ligand binding in the context of WW1-WW2 tandem module of WWOX is discussed. Notably, the WW domains within the WW1-WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. In this manner, the association of WW2 domain with WW1 hinders ligand binding to the latter. Consequently, ligand binding to WW1 domain not only results in the displacement of WW2 lid but also disrupts the fixed orientation of WW domains in the liganded conformation. Equally importantly, structure-guided functional approach suggests that the catalytic domain of WWOX likely serves as a retinal oxidoreductase that catalyzes the reversible oxidation and reduction of all-trans-retinal. Collectively, this review provides structural insights into the functional versatility of a key signaling protein with important implications on its biology. © 2015 by the Society for Experimental Biology and Medicine.

Configuration of ripple domains and their topological defects formed under local mechanical stress on hexagonal monolayer graphene.

PubMed

Park, Yeonggu; Choi, Jin Sik; Choi, Taekjib; Lee, Mi Jung; Jia, Quanxi; Park, Minwoo; Lee, Hoonkyung; Park, Bae Ho

2015-03-24

Ripples in graphene are extensively investigated because they ensure the mechanical stability of two-dimensional graphene and affect its electronic properties. They arise from spontaneous symmetry breaking and are usually manifested in the form of domains with long-range order. It is expected that topological defects accompany a material exhibiting long-range order, whose functionality depends on characteristics of domains and topological defects. However, there remains a lack of understanding regarding ripple domains and their topological defects formed on monolayer graphene. Here we explore configuration of ripple domains and their topological defects in exfoliated monolayer graphenes on SiO2/Si substrates using transverse shear microscope. We observe three-color domains with three different ripple directions, which meet at a core. Furthermore, the closed domain is surrounded by an even number of cores connected together by domain boundaries, similar to topological vortex and anti-vortex pairs. In addition, we have found that axisymmetric three-color domains can be induced around nanoparticles underneath the graphene. This fascinating configuration of ripple domains may result from the intrinsic hexagonal symmetry of two-dimensional graphene, which is supported by theoretical simulation using molecular dynamics. Our findings are expected to play a key role in understanding of ripple physics in graphene and other two-dimensional materials.

Cohesin and related coiled-coil domain-containing complexes physically and functionally connect the dots across the genome

PubMed Central

Poon, Betty P.K

2011-01-01

Interactions between genetic regions located across the genome maintain its three-dimensional organization and function. Recent studies point to key roles for a set of coiled-coil domain-containing complexes (cohibin, cohesin, condensin and monopolin) and related factors in the regulation of DNA-DNA connections across the genome. These connections are critical to replication, recombination, gene expression as well as chromosome segregation. PMID:21822055

A novel method for inverse fiber Bragg grating structure design

NASA Astrophysics Data System (ADS)

Yin, Yu-zhe; Chen, Xiang-fei; Dai, Yi-tang; Xie, Shi-zhong

2003-12-01

A novel grating inverse design method is proposed in this paper, which is direct in physical meaning and easy to accomplish. The key point of the method is design and implement desired spectra response in grating strength modulation domain, while not in grating period chirp domain. Simulated results are in good coincidence with design target. By transforming grating period chirp to grating strength modulation, a novel grating with opposite dispersion characters is proposed.

A knowledge-driven approach to biomedical document conceptualization.

PubMed

Zheng, Hai-Tao; Borchert, Charles; Jiang, Yong

2010-06-01

Biomedical document conceptualization is the process of clustering biomedical documents based on ontology-represented domain knowledge. The result of this process is the representation of the biomedical documents by a set of key concepts and their relationships. Most of clustering methods cluster documents based on invariant domain knowledge. The objective of this work is to develop an effective method to cluster biomedical documents based on various user-specified ontologies, so that users can exploit the concept structures of documents more effectively. We develop a flexible framework to allow users to specify the knowledge bases, in the form of ontologies. Based on the user-specified ontologies, we develop a key concept induction algorithm, which uses latent semantic analysis to identify key concepts and cluster documents. A corpus-related ontology generation algorithm is developed to generate the concept structures of documents. Based on two biomedical datasets, we evaluate the proposed method and five other clustering algorithms. The clustering results of the proposed method outperform the five other algorithms, in terms of key concept identification. With respect to the first biomedical dataset, our method has the F-measure values 0.7294 and 0.5294 based on the MeSH ontology and gene ontology (GO), respectively. With respect to the second biomedical dataset, our method has the F-measure values 0.6751 and 0.6746 based on the MeSH ontology and GO, respectively. Both results outperforms the five other algorithms in terms of F-measure. Based on the MeSH ontology and GO, the generated corpus-related ontologies show informative conceptual structures. The proposed method enables users to specify the domain knowledge to exploit the conceptual structures of biomedical document collections. In addition, the proposed method is able to extract the key concepts and cluster the documents with a relatively high precision. Copyright 2010 Elsevier B.V. All rights reserved.

Structural And Functional Studies of ALIX Interactions With YPXnL Late Domains of HIV-1 And EIAV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhai, Q.; Fisher, R.D.; Chung, H.-Y.

2009-05-28

Retrovirus budding requires short peptide motifs (late domains) located within the viral Gag protein that function by recruiting cellular factors. The YPX{sub n}L late domains of HIV and other lentiviruses recruit the protein ALIX (also known as AIP1), which also functions in vesicle formation at the multivesicular body and in the abscission stage of cytokinesis. Here, we report the crystal structures of ALIX in complex with the YPX{sub n}L late domains from HIV-1 and EIAV. The two distinct late domains bind at the same site on the ALIX V domain but adopt different conformations that allow them to make equivalentmore » contacts. Binding studies and functional assays verified the importance of key interface residues and revealed that binding affinities are tuned by context-dependent effects. These results reveal how YPX{sub n}L late domains recruit ALIX to facilitate virus budding and how ALIX can bind YPX{sub n}L sequences with both n = 1 and n = 3.« less

The Phe105 loop of Alix Bro1 domain plays a key role in HIV-1 release

PubMed Central

Sette, Paola; Mu, Ruiling; Dussupt, Vincent; Jiang, Jiansheng; Snyder, Greg; Smith, Patrick; Xiao, Tsan. Sam; Bouamr, Fadila

2011-01-01

Summary Alix and cellular paralogs HD-PTP and Brox contain N-terminal Bro1 domains that bind ESCRT-III CHMP4. In contrast to HD-PTP and Brox, expression of the Bro1 domain of Alix alleviates HIV-1 release defects due to interrupted access to ESCRT. In an attempt to elucidate this functional discrepancy, we solved the crystal structures of the Bro1 domains of HD-PTP and Brox. They revealed typical “boomerang” folds they share with the Bro1 Alix domain. However, they each contain unique structural features that may be relevant to their specific function(s). In particular, phenylalanine residue in position 105 (Phe105) of Alix belongs to a long loop that is unique to its Bro1 domain. Concurrently mutation of Phe105 and surrounding residues at the tip of the loop compromises the function of Alix in HIV-1 budding without affecting its interactions with Gag or CHMP4. These studies identify a new functional determinant in the Bro1 domain of Alix. PMID:21889351

An effective and secure key-management scheme for hierarchical access control in E-medicine system.

PubMed

Odelu, Vanga; Das, Ashok Kumar; Goswami, Adrijit

2013-04-01

Recently several hierarchical access control schemes are proposed in the literature to provide security of e-medicine systems. However, most of them are either insecure against 'man-in-the-middle attack' or they require high storage and computational overheads. Wu and Chen proposed a key management method to solve dynamic access control problems in a user hierarchy based on hybrid cryptosystem. Though their scheme improves computational efficiency over Nikooghadam et al.'s approach, it suffers from large storage space for public parameters in public domain and computational inefficiency due to costly elliptic curve point multiplication. Recently, Nikooghadam and Zakerolhosseini showed that Wu-Chen's scheme is vulnerable to man-in-the-middle attack. In order to remedy this security weakness in Wu-Chen's scheme, they proposed a secure scheme which is again based on ECC (elliptic curve cryptography) and efficient one-way hash function. However, their scheme incurs huge computational cost for providing verification of public information in the public domain as their scheme uses ECC digital signature which is costly when compared to symmetric-key cryptosystem. In this paper, we propose an effective access control scheme in user hierarchy which is only based on symmetric-key cryptosystem and efficient one-way hash function. We show that our scheme reduces significantly the storage space for both public and private domains, and computational complexity when compared to Wu-Chen's scheme, Nikooghadam-Zakerolhosseini's scheme, and other related schemes. Through the informal and formal security analysis, we further show that our scheme is secure against different attacks and also man-in-the-middle attack. Moreover, dynamic access control problems in our scheme are also solved efficiently compared to other related schemes, making our scheme is much suitable for practical applications of e-medicine systems.

Conservation of the Human Integrin-Type Beta-Propeller Domain in Bacteria

PubMed Central

Chouhan, Bhanupratap; Denesyuk, Alexander; Heino, Jyrki; Johnson, Mark S.; Denessiouk, Konstantin

2011-01-01

Integrins are heterodimeric cell-surface receptors with key functions in cell-cell and cell-matrix adhesion. Integrin α and β subunits are present throughout the metazoans, but it is unclear whether the subunits predate the origin of multicellular organisms. Several component domains have been detected in bacteria, one of which, a specific 7-bladed β-propeller domain, is a unique feature of the integrin α subunits. Here, we describe a structure-derived motif, which incorporates key features of each blade from the X-ray structures of human αIIbβ3 and αVβ3, includes elements of the FG-GAP/Cage and Ca2+-binding motifs, and is specific only for the metazoan integrin domains. Separately, we searched for the metazoan integrin type β-propeller domains among all available sequences from bacteria and unicellular eukaryotic organisms, which must incorporate seven repeats, corresponding to the seven blades of the β-propeller domain, and so that the newly found structure-derived motif would exist in every repeat. As the result, among 47 available genomes of unicellular eukaryotes we could not find a single instance of seven repeats with the motif. Several sequences contained three repeats, a predicted transmembrane segment, and a short cytoplasmic motif associated with some integrins, but otherwise differ from the metazoan integrin α subunits. Among the available bacterial sequences, we found five examples containing seven sequential metazoan integrin-specific motifs within the seven repeats. The motifs differ in having one Ca2+-binding site per repeat, whereas metazoan integrins have three or four sites. The bacterial sequences are more conserved in terms of motif conservation and loop length, suggesting that the structure is more regular and compact than those example structures from human integrins. Although the bacterial examples are not full-length integrins, the full-length metazoan-type 7-bladed β-propeller domains are present, and sometimes two tandem copies are found. PMID:22022374

Using theory to explore facilitators and barriers to delayed prescribing in Australia: a qualitative study using the Theoretical Domains Framework and the Behaviour Change Wheel.

PubMed

Sargent, Lucy; McCullough, Amanda; Del Mar, Chris; Lowe, John

2017-02-13

Delayed antibiotic prescribing reduces antibiotic use for acute respiratory infections in trials in general practice, but the uptake in clinical practice is low. The aim of the study was to identify facilitators and barriers to general practitioners' (GPs') use of delayed prescribing and to gain pharmacists' and the public's views about delayed prescribing in Australia. This study used the Theoretical Domains Framework and the Behaviour Change Wheel to explore facilitators and barriers to delayed prescribing in Australia. Forty-three semi-structured, face-to-face interviews with general practitioners, pharmacists and patients were conducted. Responses were coded into domains of the Theoretical Domains Framework, and specific criteria from the Behaviour Change Wheel were used to identify which domains were relevant to increasing the use of delayed prescribing by GPs. The interviews revealed nine key domains that influence GPs' use of delayed prescribing: knowledge; cognitive and interpersonal skills; memory, attention and decision-making processes; optimism; beliefs about consequences; intentions; goals; emotion; and social influences: GPs knew about delayed prescribing; however, they did not use it consistently, preferring to bring patients back for review and only using it with patients in a highly selective way. Pharmacists would support GPs and the public in delayed prescribing but would fill the prescription if people insisted. The public said they would delay taking their antibiotics if asked by their GP and given the right information on managing symptoms and when to take antibiotics. Using a theory-driven approach, we identified nine key domains that influence GPs' willingness to provide a delayed prescription to patients with an acute respiratory infection presenting to general practice. These data can be used to develop a structured intervention to change this behaviour and thus reduce antibiotic use for acute respiratory infections in general practice.

Threading structural model of the manganese-stabilizing protein PsbO reveals presence of two possible beta-sandwich domains.

PubMed

Pazos, F; Heredia, P; Valencia, A; de las Rivas, J

2001-12-01

The manganese-stabilizing protein (PsbO) is an essential component of photosystem II (PSII) and is present in all oxyphotosynthetic organisms. PsbO allows correct water splitting and oxygen evolution by stabilizing the reactions driven by the manganese cluster. Despite its important role, its structure and detailed functional mechanism are still unknown. In this article we propose a structural model based on fold recognition and molecular modeling. This model has additional support from a study of the distribution of characteristics of the PsbO sequence family, such as the distribution of conserved, apolar, tree-determinants, and correlated positions. Our threading results consistently showed PsbO as an all-beta (beta) protein, with two homologous beta domains of approximately 120 amino acids linked by a flexible Proline-Glycine-Glycine (PGG) motif. These features are compatible with a general elongated and flexible architecture, in which the two domains form a sandwich-type structure with Greek key topology. The first domain is predicted to include 8 to 9 beta-strands, the second domain 6 to 7 beta-strands. An Ig-like beta-sandwich structure was selected as a template to build the 3-D model. The second domain has, between the strands, long-loops rich in Pro and Gly that are difficult to model. One of these long loops includes a highly conserved region (between P148 and P174) and a short alpha-helix (between E181 and N188)). These regions are characteristic parts of PsbO and show that the second domain is not so similar to the template. Overall, the model was able to account for much of the experimental data reported by several authors, and it would allow the detection of key residues and regions that are proposed in this article as essential for the structure and function of PsbO. Copyright 2001 Wiley-Liss, Inc.

Sensing voltage across lipid membranes

PubMed Central

Swartz, Kenton J.

2009-01-01

The detection of electrical potentials across lipid bilayers by specialized membrane proteins is required for many fundamental cellular processes such as the generation and propagation of nerve impulses. These membrane proteins possess modular voltage-sensing domains, a notable example being the S1-S4 domains of voltage-activated ion channels. Ground-breaking structural studies on these domains explain how voltage sensors are designed and reveal important interactions with the surrounding lipid membrane. Although further structures are needed to fully understand the conformational changes that occur during voltage sensing, the available data help to frame several key concepts that are fundamental to the mechanism of voltage sensing. PMID:19092925

Partners in crime: The role of tandem modules in gene transcription.

PubMed

Sharma, Rajal; Zhou, Ming-Ming

2015-09-01

Histones and their modifications play an important role in the regulation of gene transcription. Numerous modifications, such as acetylation, phosphorylation, methylation, ubiquitination, and SUMOylation, have been described. These modifications almost always co-occur and thereby increase the combinatorial complexity of post-translational modification detection. The domains that recognize these histone modifications often occur in tandem in the context of larger proteins and complexes. The presence of multiple modifications can positively or negatively regulate the binding of these tandem domains, influencing downstream cellular function. Alternatively, these tandem domains can have novel functions from their independent parts. Here we summarize structural and functional information known about major tandem domains and their histone binding properties. An understanding of these interactions is key for the development of epigenetic therapy. © 2015 The Protein Society.

Molecular Interaction Between Smurfl WW2 Domain and PPXY Motifs of Smadl, Smad5, and Smad6-Modeling and Analysis.

PubMed

Sangadala, Sreedhara; Rao Metpally, Raghu Prasad; B Reddy, Boojala Vijay

2007-08-01

Abstract The ubiquitin-proteasome proteolytic pathway is essential for various important biological processes including cell cycle progression, gene transcription, and signal transduction. One of the important regulatory mechanisms by which the bone-inducing activity of the bone morphogenetic protein (BMP) signaling is modulated involves ubiquitin-mediated proteasomal degradation. The BMP induced receptor signal is transmitted intracellularly by phosphorylation of Smad proteins by the activated receptor I. The phosphorylated Smads 1, 5, and 8 (R-Smads) oligomerize with the co-Smad (Smad4). The complex, thus, formed translocates to the nucleus and interacts with other cofactors to regulate the expression of downstream target genes. R-Smads contain PPXY motif in the linker region that interacts with Smad ubiquitin regulatory factor 1 (Smurf1), an E3 ubiquitin ligase that catalyzes ubiquitination of target proteins for proteasomal degradation. Smurf1 contains a HECT domain, a C2 domain, and 2 WW domains (WW1, WW2). The PPXY motif in target proteins and its interaction with Smurf1 may form the basis for regulation of steady-state levels of Smads in controlling BMP-responsiveness of cells. Here, we present a homology-based model of the Smurf1 WW2 domain and the target octa-peptides containing PPXY motif of Smurf1- interacting Smads. We carried out docking of Smurf1 WW2 domain with the PPXY motifs of Smadl, Smad5, and Smad6 and identified the key amino acid residues involved in interaction. Furthermore, we present experimental evidence that WW2 domain of Smurf1 does indeed interact with the Smad proteins and that the deletion of WW2 domain of Smurf1 results in loss of its binding to Smads using the purified recombinant proteins. Finally, we also present data confirming that the deletion of WW2 domain in Smurf1 abolishes its ubiquitination activity on Smad1 in an in vitro ubiquitination assay. It shows that the interaction between the WW domain and Smad PPXY motif is a key step in Smurf1-mediated ubiquitination of its natural targets such as Smad1, Smad5, and Smad6. This work facilitates further strategies to unravel the biological function of such interactions and help in designing effective mimetic compounds that either mimic or disrupt the specific interaction.

Molecular interaction between Smurf1 WW2 domain and PPXY motifs of Smad1, Smad5, and Smad6--modeling and analysis.

PubMed

Sangadala, Sreedhara; Metpally, Raghu Prasad Rao; Reddy, Boojala Vijay B

2007-08-01

The ubiquitin-proteasome proteolytic pathway is essential for various important biological processes including cell cycle progression, gene transcription, and signal transduction. One of the important regulatory mechanisms by which the bone-inducing activity of the bone morphogenetic protein (BMP) signaling is modulated involves ubiquitin-mediated proteasomal degradation. The BMP induced receptor signal is transmitted intracellularly by phosphorylation of Smad proteins by the activated receptor I. The phosphorylated Smads 1, 5, and 8 (R-Smads) oligomerize with the co-Smad (Smad4). The complex, thus, formed translocates to the nucleus and interacts with other cofactors to regulate the expression of downstream target genes. R-Smads contain PPXY motif in the linker region that interacts with Smad ubiquitin regulatory factor 1 (Smurf1), an E3 ubiquitin ligase that catalyzes ubiquitination of target proteins for proteasomal degradation. Smurf1 contains a HECT domain, a C2 domain, and 2 WW domains (WW1, WW2). The PPXY motif in target proteins and its interaction with Smurf1 may form the basis for regulation of steady-state levels of Smads in controlling BMP-responsiveness of cells. Here, we present a homology-based model of the Smurf1 WW2 domain and the target octa-peptides containing PPXY motif of Smurf1-interacting Smads. We carried out docking of Smurf1 WW2 domain with the PPXY motifs of Smad1, Smad5, and Smad6 and identified the key amino acid residues involved in interaction. Furthermore, we present experimental evidence that WW2 domain of Smurf1 does indeed interact with the Smad proteins and that the deletion of WW2 domain of Smurf1 results in loss of its binding to Smads using the purified recombinant proteins. Finally, we also present data confirming that the deletion of WW2 domain in Smurf1 abolishes its ubiquitination activity on Smad1 in an in vitro ubiquitination assay. It shows that the interaction between the WW domain and Smad PPXY motif is a key step in Smurf1-mediated ubiquitination of its natural targets such as Smad1, Smad5, and Smad6. This work facilitates further strategies to unravel the biological function of such interactions and help in designing effective mimetic compounds that either mimic or disrupt the specific interaction.

A hybrid two-component system protein from Azospirillum brasilense Sp7 was involved in chemotaxis.

PubMed

Cui, Yanhua; Tu, Ran; Wu, Lixian; Hong, Yuanyuan; Chen, Sanfeng

2011-09-20

We here report the sequence and functional analysis of org35 of Azospirillum brasilense Sp7, which was originally identified to be able to interact with NifA in yeast-two-hybrid system. The org35 encodes a hybrid two-component system protein, including N-terminal PAS domains, a histidine kinase (HPK) domain and a response regulator (RR) domain in C-terminal. To determine the function of the Org35, a deletion-insertion mutant in PAS domain [named Sp7353] and a complemental strain Sp7353C were constructed. The mutant had reduced chemotaxis ability compared to that of wild-type, and the complemental strain was similar to the wild-type strain. These data suggested that the A. brasilense org35 played a key role in chemotaxis. Variants containing different domains of the org35 were expressed, and the functions of these domains were studied in vitro. Phosphorylation assays in vitro demonstrated that the HPK domain of Org35 possessed the autokinase activity and that the phosphorylated HPK was able to transfer phosphate groups to the RR domain. The result indicated Org35 was a phosphorylation-communicating protein. Copyright © 2010 Elsevier GmbH. All rights reserved.

Tunable short-wavelength spin wave excitation from pinned magnetic domain walls

PubMed Central

Van de Wiele, Ben; Hämäläinen, Sampo J.; Baláž, Pavel; Montoncello, Federico; van Dijken, Sebastiaan

2016-01-01

Miniaturization of magnonic devices for wave-like computing requires emission of short-wavelength spin waves, a key feature that cannot be achieved with microwave antennas. In this paper, we propose a tunable source of short-wavelength spin waves based on highly localized and strongly pinned magnetic domain walls in ferroelectric-ferromagnetic bilayers. When driven into oscillation by a microwave spin-polarized current, the magnetic domain walls emit spin waves with the same frequency as the excitation current. The amplitude of the emitted spin waves and the range of attainable excitation frequencies depend on the availability of domain wall resonance modes. In this respect, pinned domain walls in magnetic nanowires are particularly attractive. In this geometry, spin wave confinement perpendicular to the nanowire axis produces a multitude of domain wall resonances enabling efficient spin wave emission at frequencies up to 100 GHz and wavelengths down to 20 nm. At high frequency, the emission of spin waves in magnetic nanowires becomes monochromatic. Moreover, pinning of magnetic domain wall oscillators onto the same ferroelectric domain boundary in parallel nanowires guarantees good coherency between spin wave sources, which opens perspectives towards the realization of Mach-Zehnder type logic devices and sensors. PMID:26883893

Lune/eye gone, a Pax-like protein, uses a partial paired domain and a homeodomain for DNA recognition.

PubMed

Jun, S; Wallen, R V; Goriely, A; Kalionis, B; Desplan, C

1998-11-10

Pax proteins, characterized by the presence of a paired domain, play key regulatory roles during development. The paired domain is a bipartite DNA-binding domain that contains two helix-turn-helix domains joined by a linker region. Each of the subdomains, the PAI and RED domains, has been shown to be a distinct DNA-binding domain. The PAI domain is the most critical, but in specific circumstances, the RED domain is involved in DNA recognition. We describe a Pax protein, originally called Lune, that is the product of the Drosophila eye gone gene (eyg). It is unique among Pax proteins, because it contains only the RED domain. eyg seems to play a role both in the organogenesis of the salivary gland during embryogenesis and in the development of the eye. A high-affinity binding site for the Eyg RED domain was identified by using systematic evolution of ligands by exponential enrichment techniques. This binding site is related to a binding site previously identified for the RED domain of the Pax-6 5a isoform. Eyg also contains another DNA-binding domain, a Prd-class homeodomain (HD), whose palindromic binding site is similar to other Prd-class HDs. The ability of Pax proteins to use the PAI, RED, and HD, or combinations thereof, may be one mechanism that allows them to be used at different stages of development to regulate various developmental processes through the activation of specific target genes.

Lune/eye gone, a Pax-like protein, uses a partial paired domain and a homeodomain for DNA recognition

PubMed Central

Jun, Susie; Wallen, Robert V.; Goriely, Anne; Kalionis, Bill; Desplan, Claude

1998-01-01

Pax proteins, characterized by the presence of a paired domain, play key regulatory roles during development. The paired domain is a bipartite DNA-binding domain that contains two helix–turn–helix domains joined by a linker region. Each of the subdomains, the PAI and RED domains, has been shown to be a distinct DNA-binding domain. The PAI domain is the most critical, but in specific circumstances, the RED domain is involved in DNA recognition. We describe a Pax protein, originally called Lune, that is the product of the Drosophila eye gone gene (eyg). It is unique among Pax proteins, because it contains only the RED domain. eyg seems to play a role both in the organogenesis of the salivary gland during embryogenesis and in the development of the eye. A high-affinity binding site for the Eyg RED domain was identified by using systematic evolution of ligands by exponential enrichment techniques. This binding site is related to a binding site previously identified for the RED domain of the Pax-6 5a isoform. Eyg also contains another DNA-binding domain, a Prd-class homeodomain (HD), whose palindromic binding site is similar to other Prd-class HDs. The ability of Pax proteins to use the PAI, RED, and HD, or combinations thereof, may be one mechanism that allows them to be used at different stages of development to regulate various developmental processes through the activation of specific target genes. PMID:9811867

A residue-specific shift in stability and amyloidogenicity of antibody variable domains.

PubMed

Nokwe, Cardine N; Zacharias, Martin; Yagi, Hisashi; Hora, Manuel; Reif, Bernd; Goto, Yuji; Buchner, Johannes

2014-09-26

Variable (V) domains of antibodies are essential for antigen recognition by our adaptive immune system. However, some variants of the light chain V domains (VL) form pathogenic amyloid fibrils in patients. It is so far unclear which residues play a key role in governing these processes. Here, we show that the conserved residue 2 of VL domains is crucial for controlling its thermodynamic stability and fibril formation. Hydrophobic side chains at position 2 stabilize the domain, whereas charged residues destabilize and lead to amyloid fibril formation. NMR experiments identified several segments within the core of the VL domain to be affected by changes in residue 2. Furthermore, molecular dynamic simulations showed that hydrophobic side chains at position 2 remain buried in a hydrophobic pocket, and charged side chains show a high flexibility. This results in a predicted difference in the dissociation free energy of ∼10 kJ mol(-1), which is in excellent agreement with our experimental values. Interestingly, this switch point is found only in VL domains of the κ family and not in VLλ or in VH domains, despite a highly similar domain architecture. Our results reveal novel insight into the architecture of variable domains and the prerequisites for formation of amyloid fibrils. This might also contribute to the rational design of stable variable antibody domains. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Molecular and thermodynamic mechanisms of the chloride-dependent human angiotensin-I-converting enzyme (ACE).

PubMed

Yates, Christopher J; Masuyer, Geoffrey; Schwager, Sylva L U; Akif, Mohd; Sturrock, Edward D; Acharya, K Ravi

2014-01-17

Somatic angiotensin-converting enzyme (sACE), a key regulator of blood pressure and electrolyte fluid homeostasis, cleaves the vasoactive angiotensin-I, bradykinin, and a number of other physiologically relevant peptides. sACE consists of two homologous and catalytically active N- and C-domains, which display marked differences in substrate specificities and chloride activation. A series of single substitution mutants were generated and evaluated under varying chloride concentrations using isothermal titration calorimetry. The x-ray crystal structures of the mutants provided details on the chloride-dependent interactions with ACE. Chloride binding in the chloride 1 pocket of C-domain ACE was found to affect positioning of residues from the active site. Analysis of the chloride 2 pocket R522Q and R522K mutations revealed the key interactions with the catalytic site that are stabilized via chloride coordination of Arg(522). Substrate interactions in the S2 subsite were shown to affect chloride affinity in the chloride 2 pocket. The Glu(403)-Lys(118) salt bridge in C-domain ACE was shown to stabilize the hinge-bending region and reduce chloride affinity by constraining the chloride 2 pocket. This work demonstrated that substrate composition to the C-terminal side of the scissile bond as well as interactions of larger substrates in the S2 subsite moderate chloride affinity in the chloride 2 pocket of the ACE C-domain, providing a rationale for the substrate-selective nature of chloride dependence in ACE and how this varies between the N- and C-domains.

Molecular and Thermodynamic Mechanisms of the Chloride-dependent Human Angiotensin-I-converting Enzyme (ACE)*

PubMed Central

Yates, Christopher J.; Masuyer, Geoffrey; Schwager, Sylva L. U.; Akif, Mohd; Sturrock, Edward D.; Acharya, K. Ravi

2014-01-01

Somatic angiotensin-converting enzyme (sACE), a key regulator of blood pressure and electrolyte fluid homeostasis, cleaves the vasoactive angiotensin-I, bradykinin, and a number of other physiologically relevant peptides. sACE consists of two homologous and catalytically active N- and C-domains, which display marked differences in substrate specificities and chloride activation. A series of single substitution mutants were generated and evaluated under varying chloride concentrations using isothermal titration calorimetry. The x-ray crystal structures of the mutants provided details on the chloride-dependent interactions with ACE. Chloride binding in the chloride 1 pocket of C-domain ACE was found to affect positioning of residues from the active site. Analysis of the chloride 2 pocket R522Q and R522K mutations revealed the key interactions with the catalytic site that are stabilized via chloride coordination of Arg522. Substrate interactions in the S2 subsite were shown to affect chloride affinity in the chloride 2 pocket. The Glu403-Lys118 salt bridge in C-domain ACE was shown to stabilize the hinge-bending region and reduce chloride affinity by constraining the chloride 2 pocket. This work demonstrated that substrate composition to the C-terminal side of the scissile bond as well as interactions of larger substrates in the S2 subsite moderate chloride affinity in the chloride 2 pocket of the ACE C-domain, providing a rationale for the substrate-selective nature of chloride dependence in ACE and how this varies between the N- and C-domains. PMID:24297181

Preliminary identification of key clinical domains for outcome evaluation in fibromyalgia using the Delphi method: the Italian experience.

PubMed

Salaffi, F; Ciapetti, A; Sarzi Puttini, P; Atzeni, F; Iannuccelli, C; Di Franco, M; Cazzola, M; Bazzichi, L

2012-03-19

Fibromyalgia (FM) is a complex syndrome that, in Italy, affects at least 2% of the adult population. It is characterized by chronic widespread musculoskeletal pain often accompanied by multiple other symptoms. The aim of this study was to identify a set of clinical domains for FM considered relevant by both clinicians and patients using a consensus process. Consensus was achieved using the Delphi method based on questionnaires and systematic, controlled opinion feedback. The Delphi exercise involved a panel of 252 rheumatologists and 86 patients with FM as defined by the American College of Rheumatology criteria. All of the patients and clinicians were asked to rank the relative different domains of FM in order of priority. The content validity index (CVI) was used to establish the percentage agreement. The importance of each item was ranked on a 0-3 Likert scale. The frequency, mean relevance scores, and frequency importance product were also calculated. The Delphi exercise showed that the domains ranked highest by patients were similar to those of the clinicians, with the exception of tender point intensity (considered relevant by the clinicians but not by the patients) and environmental sensitivity (considered important by the patients but not by the clinicians). A final 8-item model was developed which was considered to demonstrate adequate validity. The Delphi exercises identified and ranked relevant key clinical domains that need to be assessed in FM research. On the basis of these results, a new patient-reported composite outcome index can be developed and used in clinical trials.

The E-Business Opportunity: A Key Role for Business Educators.

ERIC Educational Resources Information Center

McGrath, Leanne C.; Lomerson, William L.

2001-01-01

Outlines considerations for pursuing electronic business: website content; cost of authoring, hosting, and registering domains; design (usability, aesthetics, functionality, confidentiality); customer focus; marketing; and maintenance. (Contains 29 references.) (SK)

Satellite observation analysis of aerosols loading effect over Monrovia-Liberia

NASA Astrophysics Data System (ADS)

Emetere, M. E.; Esisio, F.; Oladapo, F.

2017-05-01

The effect of aerosols loading most often results in aerosols retention in the atmosphere. Aside the health hazards of aerosol retention, its effect on climate change are visible. In this research, it was proposed that the effect of aerosol retention also affects rain pattern. The Tropical Rainfall Measuring Mission (TRMM) layer 3 observations and the multi-imaging spectro-reflectometer (MISR) was used for the study. The aerosols loading over were investigated using sixteen years satellite observation in Monrovia-Liberia. Its effect on the rain rate over the region was documented. The results show that aerosol loading over the region is high and may have effect on farming in the nearest future. It was affirmed that the scanty AOD data was as a result of the rain rate that is higher within May and October.

AmeriFlux Measurement Component (AMC) Instrument Handbook

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reichl, Ken; Biraud, Sebastien C.

2016-04-01

An AMC system was installed at the U.S. Department of Energy (DOE)’s Atmospheric Radiation Measurement (ARM) Climate Research Facility North Slope of Alaska (NSA) Barrow site, also known as NSA C1 at the ARM Data Archive, in August 2012. A second AMC system was installed at the third ARM Mobile Facility deployment at Oliktok Point, also known as NSA M1. This in situ system consists of 12 combination soil temperature and volumetric water content (VWC) reflectometers and one set of upwelling and downwelling photosynthetically active radiation (PAR) sensors, all deployed within the fetch of the Eddy Correlation Flux Measurement System.more » Soil temperature and VWC sensors placed at two depths (10 and 30 cm below the vegetation layer) at six locations (or microsites) allow soil property inhomogeneity to be monitored across a landscape.« less

[Blood-sugar self control. A means for the diabetic of controlling his metabolic management. Quality control of a battery-run pocket size reflectometer (glucose-meter)].

PubMed

Leidinger, F; Jörgens, V; Chantelau, E; Berchtold, P; Berger, M

1980-07-26

Home blood glucose monitoring by diabetic patients has recently been advocated as an effective means to improve metabolic control. The Glucocheck apparatus, a pocket-size battery-driven reflectance-meter (in Germany commercially available under the name Glucose-meter), has been evaluated for accuracy and practicability. In 450 blood glucose measurements, the variance between the values obtained using the Glucocheck apparatus and routine clinical laboratory procedures was +/- 11.7%. Especially in the low range of blood glucose concentrations, the Glucocheck method was very reliable. The quantitative precision of the Glucocheck method depends, however, quite considerably on the ability of the patient to use the apparatus correctly. In order to profit from Glucocheck in clinical practice, particular efforts to educate the patients in its use are necessary.

Wafer characteristics via reflectometry

DOEpatents

Sopori, Bhushan L.

2010-10-19

Various exemplary methods (800, 900, 1000, 1100) are directed to determining wafer thickness and/or wafer surface characteristics. An exemplary method (900) includes measuring reflectance of a wafer and comparing the measured reflectance to a calculated reflectance or a reflectance stored in a database. Another exemplary method (800) includes positioning a wafer on a reflecting support to extend a reflectance range. An exemplary device (200) has an input (210), analysis modules (222-228) and optionally a database (230). Various exemplary reflectometer chambers (1300, 1400) include radiation sources positioned at a first altitudinal angle (1308, 1408) and at a second altitudinal angle (1312, 1412). An exemplary method includes selecting radiation sources positioned at various altitudinal angles. An exemplary element (1650, 1850) includes a first aperture (1654, 1854) and a second aperture (1658, 1858) that can transmit reflected radiation to a fiber and an imager, respectfully.

Space Science Payloads Optical Properties Monitor (OPM) Mission Flight Anomalies Thermal Analyses

NASA Technical Reports Server (NTRS)

Schmitz, Craig P.

2001-01-01

The OPM was the first space payload that measured in-situ the optical properties of materials and had data telemetered to ground. The OPM was EVA mounted to the Mir Docking Module for an eight-month stay where flight samples were exposed to the Mir induced and natural environments. The OPM was comprised of three optical instruments; a total hemispherical spectral reflectometer, a vacuum ultraviolet spectrometer, and a total integrated scatterometer. There were also three environmental monitors; an atomic oxygen monitor, solar and infrared radiometers, and two temperature-controlled quartz crystal microbalances (to monitor contamination). Measurements were performed weekly and data telemetered to ground through the Mir data system. This paper will describe the OPM thermal control design and how the thermal math models were used to analyze anomalies which occurred during the space flight mission.

Magnetic compound refractive lens for focusing and polarizing cold neutron beams.

PubMed

Littrell, K C; te Velthuis, S G E; Felcher, G P; Park, S; Kirby, B J; Fitzsimmons, M R

2007-03-01

Biconcave cylindrical lenses are used to focus beams of x rays or neutrons using the refractive properties of matter. In the case of neutrons, the refractive properties of magnetic induction can similarly focus and simultaneously polarize the neutron beam without the concomitant attenuation of matter. This concept of a magnetic refractive lens was tested using a compound lens consisting of 99 pairs of cylindrical permanent magnets. The assembly successfully focused the intensity of a white beam of cold neutrons of one spin state at the detector, while defocusing the other. This experiment confirmed that a lens of this nature may boost the intensity locally by almost an order of magnitude and create a polarized beam. An estimate of the performance of a more practically dimensioned device suitable for incorporation in reflectometers and slit-geometry small angle scattering instruments is given.

Active cleaning technique for removing contamination from optical surfaces in space

NASA Technical Reports Server (NTRS)

Shannon, R. L.; Gillette, R. B.; Cruz, G. A.

1973-01-01

An active cleaning technique for removing contaminants from optical surfaces in space was investigated with emphasis on the feasibility of using plasma exposure as a means of in-situ cleaning. The major work accomplished includes: (1) development of an in-situ reflectometer for use in conjunction with the contaminant film deposition/cleaning facility; (2) completion of Apollo Telescope Mount (ATM) filter treatment experiments to assess the effects of plasma exposure on the UV transmittance; (3) attempts to correlate the atomic oxygen flux with cleaning rate; (4) completion of in-situ butadien contamination/plasma cleaning/UV reflectance measurement experiments; (5) carbon cleaning experiments using various gases; (6) completion of silicone contamination/cleaning experiments; and (7) experiments conducted at low chamber pressures to determine cleaning rate distribution and contamination of surfaces adjacent to those being cleaned.

A Key Claudin Extracellular Loop Domain is Critical for Epithelial Barrier Integrity

PubMed Central

Mrsny, Randall J.; Brown, G. Thomas; Gerner-Smidt, Kirsten; Buret, Andre G.; Meddings, Jon B.; Quan, Clifford; Koval, Michael; Nusrat, Asma

2008-01-01

Intercellular tight junctions (TJs) regulate epithelial barrier properties. Claudins are major structural constituents of TJs and belong to a large family of tetra-spanning membrane proteins that have two predicted extracellular loops (ELs). Given that claudin-1 is widely expressed in epithelia, we further defined the role of its EL domains in determining TJ function. The effects of several claudin-1 EL mimetic peptides on epithelial barrier structure and function were examined. Incubation of model human intestinal epithelial cells with a 27-amino acid peptide corresponding to a portion of the first EL domain (Cldn-153–80) reversibly interfered with epithelial barrier function by inducing the rearrangement of key TJ proteins: occludin, claudin-1, junctional adhesion molecule-A, and zonula occludens-1. Cldn-153–80 associated with both claudin-1 and occludin, suggesting both the direct interference with the ability of these proteins to assemble into functional TJs and their close interaction under physiological conditions. These effects were specific for Cldn-153–80, because peptides corresponding to other claudin-1 EL domains failed to influence TJ function. Furthermore, the oral administration of Cldn-153–80 to rats increased paracellular gastric permeability. Thus, the identification of a critical claudin-1 EL motif, Cldn-153–80, capable of regulating TJ structure and function, offers a useful adjunct to treatments that require drug delivery across an epithelial barrier. PMID:18349130

ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

PubMed Central

Bhasi, Ashwini; Philip, Philge; Manikandan, Vinu; Senapathy, Periannan

2009-01-01

We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/. PMID:18984624

Effective Moment Feature Vectors for Protein Domain Structures

PubMed Central

Shi, Jian-Yu; Yiu, Siu-Ming; Zhang, Yan-Ning; Chin, Francis Yuk-Lun

2013-01-01

Imaging processing techniques have been shown to be useful in studying protein domain structures. The idea is to represent the pairwise distances of any two residues of the structure in a 2D distance matrix (DM). Features and/or submatrices are extracted from this DM to represent a domain. Existing approaches, however, may involve a large number of features (100–400) or complicated mathematical operations. Finding fewer but more effective features is always desirable. In this paper, based on some key observations on DMs, we are able to decompose a DM image into four basic binary images, each representing the structural characteristics of a fundamental secondary structure element (SSE) or a motif in the domain. Using the concept of moments in image processing, we further derive 45 structural features based on the four binary images. Together with 4 features extracted from the basic images, we represent the structure of a domain using 49 features. We show that our feature vectors can represent domain structures effectively in terms of the following. (1) We show a higher accuracy for domain classification. (2) We show a clear and consistent distribution of domains using our proposed structural vector space. (3) We are able to cluster the domains according to our moment features and demonstrate a relationship between structural variation and functional diversity. PMID:24391828

The development of ORACLe: a measure of an organisation's capacity to engage in evidence-informed health policy.

PubMed

Makkar, Steve R; Turner, Tari; Williamson, Anna; Louviere, Jordan; Redman, Sally; Haynes, Abby; Green, Sally; Brennan, Sue

2016-01-14

Evidence-informed policymaking is more likely if organisations have cultures that promote research use and invest in resources that facilitate staff engagement with research. Measures of organisations' research use culture and capacity are needed to assess current capacity, identify opportunities for improvement, and examine the impact of capacity-building interventions. The aim of the current study was to develop a comprehensive system to measure and score organisations' capacity to engage with and use research in policymaking, which we entitled ORACLe (Organisational Research Access, Culture, and Leadership). We used a multifaceted approach to develop ORACLe. Firstly, we reviewed the available literature to identify key domains of organisational tools and systems that may facilitate research use by staff. We interviewed senior health policymakers to verify the relevance and applicability of these domains. This information was used to generate an interview schedule that focused on seven key domains of organisational capacity. The interview was pilot-tested within four Australian policy agencies. A discrete choice experiment (DCE) was then undertaken using an expert sample to establish the relative importance of these domains. This data was used to produce a scoring system for ORACLe. The ORACLe interview was developed, comprised of 23 questions addressing seven domains of organisational capacity and tools that support research use, including (1) documented processes for policymaking; (2) leadership training; (3) staff training; (4) research resources (e.g. database access); and systems to (5) generate new research, (6) undertake evaluations, and (7) strengthen relationships with researchers. From the DCE data, a conditional logit model was estimated to calculate total scores that took into account the relative importance of the seven domains. The model indicated that our expert sample placed the greatest importance on domains (2), (3) and (4). We utilised qualitative and quantitative methods to develop a system to assess and score organisations' capacity to engage with and apply research to policy. Our measure assesses a broad range of capacity domains and identifies the relative importance of these capacities. ORACLe data can be used by organisations keen to increase their use of evidence to identify areas for further development.

Federal Public Health Workforce Development: An Evidence-Based Approach for Defining Competencies.

PubMed

Mumford, Karen; Young, Andrea C; Nawaz, Saira

2016-01-01

This study reports the use of exploratory factor analysis to describe essential skills and knowledge for an important segment of the domestic public health workforce-Centers for Disease Control and Prevention (CDC) project officers-using an evidence-based approach to competency development and validation. A multicomponent survey was conducted. Exploratory factor analysis was used to examine the underlying domains and relationships between competency domains and key behaviors. The Cronbach α coefficient determined the reliability of the overall scale and identified factors. All domestic (US state, tribe, local, and territorial) grantees who received funding from the CDC during fiscal year 2011 to implement nonresearch prevention or intervention programs were invited to participate in a Web-based questionnaire. A total of 34 key behaviors representing knowledge, skills, and abilities, grouped in 7 domains-communication, grant administration and management, public health applied science and knowledge, program planning and development, program management, program monitoring and improvement, and organizational consultation-were examined. There were 795 responses (58% response rate). A total of 6 factors were identified with loadings of 0.40 or more for all 34 behavioral items. The Cronbach α coefficient was 0.95 overall and ranged between 0.73 and 0.91 for the factors. This study provides empirical evidence for the construct validity of 6 competencies and 34 key behaviors important for CDC project officers and serves as an important first step to evidence-driven workforce development efforts in public health.

The Wheel of Writing: A Model of the Writing Domain for the Teaching and Assessing of Writing as a Key Competency

ERIC Educational Resources Information Center

Berge, Kjell Lars; Evensen, Lars Sigfred; Thygesen, Ragnar

2016-01-01

The model presented in this article aspires to represent a theoretically valid and coherent definition and description of writing, as a basis for teaching and assessing writing as a key competency in school. It represents a critique as well as an extension of previous alternatives in that it views writing as a culturally and individually…

An Authentication and Key Management Mechanism for Resource Constrained Devices in IEEE 802.11-based IoT Access Networks.

PubMed

Kim, Ki-Wook; Han, Youn-Hee; Min, Sung-Gi

2017-09-21

Many Internet of Things (IoT) services utilize an IoT access network to connect small devices with remote servers. They can share an access network with standard communication technology, such as IEEE 802.11ah. However, an authentication and key management (AKM) mechanism for resource constrained IoT devices using IEEE 802.11ah has not been proposed as yet. We therefore propose a new AKM mechanism for an IoT access network, which is based on IEEE 802.11 key management with the IEEE 802.1X authentication mechanism. The proposed AKM mechanism does not require any pre-configured security information between the access network domain and the IoT service domain. It considers the resource constraints of IoT devices, allowing IoT devices to delegate the burden of AKM processes to a powerful agent. The agent has sufficient power to support various authentication methods for the access point, and it performs cryptographic functions for the IoT devices. Performance analysis shows that the proposed mechanism greatly reduces computation costs, network costs, and memory usage of the resource-constrained IoT device as compared to the existing IEEE 802.11 Key Management with the IEEE 802.1X authentication mechanism.

An Authentication and Key Management Mechanism for Resource Constrained Devices in IEEE 802.11-based IoT Access Networks

PubMed Central

Han, Youn-Hee; Min, Sung-Gi

2017-01-01

Many Internet of Things (IoT) services utilize an IoT access network to connect small devices with remote servers. They can share an access network with standard communication technology, such as IEEE 802.11ah. However, an authentication and key management (AKM) mechanism for resource constrained IoT devices using IEEE 802.11ah has not been proposed as yet. We therefore propose a new AKM mechanism for an IoT access network, which is based on IEEE 802.11 key management with the IEEE 802.1X authentication mechanism. The proposed AKM mechanism does not require any pre-configured security information between the access network domain and the IoT service domain. It considers the resource constraints of IoT devices, allowing IoT devices to delegate the burden of AKM processes to a powerful agent. The agent has sufficient power to support various authentication methods for the access point, and it performs cryptographic functions for the IoT devices. Performance analysis shows that the proposed mechanism greatly reduces computation costs, network costs, and memory usage of the resource-constrained IoT device as compared to the existing IEEE 802.11 Key Management with the IEEE 802.1X authentication mechanism. PMID:28934152

Added value of involving patients in the first step of multidisciplinary guideline development: a qualitative interview study among infertile patients.

PubMed

den Breejen, Elvira M E; Hermens, Rosella P M G; Galama, Wienke H; Willemsen, Wim N P; Kremer, Jan A M; Nelen, Willianne L D M

2016-06-01

Patient involvement in scoping the guideline is emphasized, but published initiatives actively involving patients are generally limited to the writing and reviewing phase. To assess patients' added value to the scoping phase of a multidisciplinary guideline on infertility. Qualitative interview study. We conducted interviews among 12 infertile couples and 17 professionals. We listed and compared the couples' and professionals' key clinical issues (=care aspects that need improvement) to be addressed in the guideline according to four domains: current guidelines, professionals, patients and organization of care. Main key clinical issues suggested by more than three quarters of the infertile couples and/or at least two professionals were identified and compared. Overall, we identified 32 key clinical issues among infertile couples and 23 among professionals. Of the defined main key clinical issues, infertile couples mentioned eight issues that were not mentioned by the professionals. These main key clinical issues mainly concerned patient-centred (e.g. poor information provision and poor alignment of care) aspects of care on the professional and organizational domain. Both groups mentioned two main key clinical issues collectively that were interpreted differently: the lack of emotional support and respect for patients' values. Including patients from the first phase of the guideline development process leads to valuable additional main key clinical issues for the next step of a multidisciplinary guideline development process and broadens the scope of the guideline, particularly regarding patient-centredness and organizational issues from a patients' perspective. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

Size and mobility of lipid domains tuned by geometrical constraints.

PubMed

Schütte, Ole M; Mey, Ingo; Enderlein, Jörg; Savić, Filip; Geil, Burkhard; Janshoff, Andreas; Steinem, Claudia

2017-07-25

In the plasma membrane of eukaryotic cells, proteins and lipids are organized in clusters, the latter ones often called lipid domains or "lipid rafts." Recent findings highlight the dynamic nature of such domains and the key role of membrane geometry and spatial boundaries. In this study, we used porous substrates with different pore radii to address precisely the extent of the geometric constraint, permitting us to modulate and investigate the size and mobility of lipid domains in phase-separated continuous pore-spanning membranes (PSMs). Fluorescence video microscopy revealed two types of liquid-ordered ( l o ) domains in the freestanding parts of the PSMs: ( i ) immobile domains that were attached to the pore rims and ( ii ) mobile, round-shaped l o domains within the center of the PSMs. Analysis of the diffusion of the mobile l o domains by video microscopy and particle tracking showed that the domains' mobility is slowed down by orders of magnitude compared with the unrestricted case. We attribute the reduced mobility to the geometric confinement of the PSM, because the drag force is increased substantially due to hydrodynamic effects generated by the presence of these boundaries. Our system can serve as an experimental test bed for diffusion of 2D objects in confined geometry. The impact of hydrodynamics on the mobility of enclosed lipid domains can have great implications for the formation and lateral transport of signaling platforms.

mlCAF: Multi-Level Cross-Domain Semantic Context Fusioning for Behavior Identification.

PubMed

Razzaq, Muhammad Asif; Villalonga, Claudia; Lee, Sungyoung; Akhtar, Usman; Ali, Maqbool; Kim, Eun-Soo; Khattak, Asad Masood; Seung, Hyonwoo; Hur, Taeho; Bang, Jaehun; Kim, Dohyeong; Ali Khan, Wajahat

2017-10-24

The emerging research on automatic identification of user's contexts from the cross-domain environment in ubiquitous and pervasive computing systems has proved to be successful. Monitoring the diversified user's contexts and behaviors can help in controlling lifestyle associated to chronic diseases using context-aware applications. However, availability of cross-domain heterogeneous contexts provides a challenging opportunity for their fusion to obtain abstract information for further analysis. This work demonstrates extension of our previous work from a single domain (i.e., physical activity) to multiple domains (physical activity, nutrition and clinical) for context-awareness. We propose multi-level Context-aware Framework (mlCAF), which fuses the multi-level cross-domain contexts in order to arbitrate richer behavioral contexts. This work explicitly focuses on key challenges linked to multi-level context modeling, reasoning and fusioning based on the mlCAF open-source ontology. More specifically, it addresses the interpretation of contexts from three different domains, their fusioning conforming to richer contextual information. This paper contributes in terms of ontology evolution with additional domains, context definitions, rules and inclusion of semantic queries. For the framework evaluation, multi-level cross-domain contexts collected from 20 users were used to ascertain abstract contexts, which served as basis for behavior modeling and lifestyle identification. The experimental results indicate a context recognition average accuracy of around 92.65% for the collected cross-domain contexts.

Structural basis for different phosphoinositide specificities of the PX domains of sorting nexins regulating G-protein signaling.

PubMed

Mas, Caroline; Norwood, Suzanne J; Bugarcic, Andrea; Kinna, Genevieve; Leneva, Natalya; Kovtun, Oleksiy; Ghai, Rajesh; Ona Yanez, Lorena E; Davis, Jasmine L; Teasdale, Rohan D; Collins, Brett M

2014-10-10

Sorting nexins (SNXs) or phox homology (PX) domain containing proteins are central regulators of cell trafficking and signaling. A subfamily of PX domain proteins possesses two unique PX-associated domains, as well as a regulator of G protein-coupled receptor signaling (RGS) domain that attenuates Gαs-coupled G protein-coupled receptor signaling. Here we delineate the structural organization of these RGS-PX proteins, revealing a protein family with a modular architecture that is conserved in all eukaryotes. The one exception to this is mammalian SNX19, which lacks the typical RGS structure but preserves all other domains. The PX domain is a sensor of membrane phosphoinositide lipids and we find that specific sequence alterations in the PX domains of the mammalian RGS-PX proteins, SNX13, SNX14, SNX19, and SNX25, confer differential phosphoinositide binding preferences. Although SNX13 and SNX19 PX domains bind the early endosomal lipid phosphatidylinositol 3-phosphate, SNX14 shows no membrane binding at all. Crystal structures of the SNX19 and SNX14 PX domains reveal key differences, with alterations in SNX14 leading to closure of the binding pocket to prevent phosphoinositide association. Our findings suggest a role for alternative membrane interactions in spatial control of RGS-PX proteins in cell signaling and trafficking. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Configuration of ripple domains and their topological defects formed under local mechanical stress on hexagonal monolayer graphene

DOE PAGES

Park, Yeonggu; Choi, Jin Sik; Choi, Taekjib; ...

2015-03-24

Ripples in graphene are extensively investigated because they ensure the mechanical stability of two-dimensional graphene and affect its electronic properties. They arise from spontaneous symmetry breaking and are usually manifested in the form of domains with long-range order. It is expected that topological defects accompany a material exhibiting long-range order, whose functionality depends on characteristics of domains and topological defects. However, there remains a lack of understanding regarding ripple domains and their topological defects formed on monolayer graphene. Here we explore configuration of ripple domains and their topological defects in exfoliated monolayer graphenes on SiO₂/Si substrates using transverse shear microscope.more » We observe three-color domains with three different ripple directions, which meet at a core. Furthermore, the closed domain is surrounded by an even number of cores connected together by domain boundaries, similar to topological vortex and anti-vortex pairs. In addition, we have found that axisymmetric three-color domains can be induced around nanoparticles underneath the graphene. This fascinating configuration of ripple domains may result from the intrinsic hexagonal symmetry of two-dimensional graphene, which is supported by theoretical simulation using molecular dynamics. Our findings are expected to play a key role in understanding of ripple physics in graphene and other two-dimensional materials.« less

Configuration of ripple domains and their topological defects formed under local mechanical stress on hexagonal monolayer graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Yeonggu; Choi, Jin Sik; Choi, Taekjib

Ripples in graphene are extensively investigated because they ensure the mechanical stability of two-dimensional graphene and affect its electronic properties. They arise from spontaneous symmetry breaking and are usually manifested in the form of domains with long-range order. It is expected that topological defects accompany a material exhibiting long-range order, whose functionality depends on characteristics of domains and topological defects. However, there remains a lack of understanding regarding ripple domains and their topological defects formed on monolayer graphene. Here we explore configuration of ripple domains and their topological defects in exfoliated monolayer graphenes on SiO₂/Si substrates using transverse shear microscope.more » We observe three-color domains with three different ripple directions, which meet at a core. Furthermore, the closed domain is surrounded by an even number of cores connected together by domain boundaries, similar to topological vortex and anti-vortex pairs. In addition, we have found that axisymmetric three-color domains can be induced around nanoparticles underneath the graphene. This fascinating configuration of ripple domains may result from the intrinsic hexagonal symmetry of two-dimensional graphene, which is supported by theoretical simulation using molecular dynamics. Our findings are expected to play a key role in understanding of ripple physics in graphene and other two-dimensional materials.« less

mlCAF: Multi-Level Cross-Domain Semantic Context Fusioning for Behavior Identification

PubMed Central

Villalonga, Claudia; Lee, Sungyoung; Akhtar, Usman; Ali, Maqbool; Kim, Eun-Soo; Khattak, Asad Masood; Seung, Hyonwoo; Hur, Taeho; Kim, Dohyeong; Ali Khan, Wajahat

2017-01-01

The emerging research on automatic identification of user’s contexts from the cross-domain environment in ubiquitous and pervasive computing systems has proved to be successful. Monitoring the diversified user’s contexts and behaviors can help in controlling lifestyle associated to chronic diseases using context-aware applications. However, availability of cross-domain heterogeneous contexts provides a challenging opportunity for their fusion to obtain abstract information for further analysis. This work demonstrates extension of our previous work from a single domain (i.e., physical activity) to multiple domains (physical activity, nutrition and clinical) for context-awareness. We propose multi-level Context-aware Framework (mlCAF), which fuses the multi-level cross-domain contexts in order to arbitrate richer behavioral contexts. This work explicitly focuses on key challenges linked to multi-level context modeling, reasoning and fusioning based on the mlCAF open-source ontology. More specifically, it addresses the interpretation of contexts from three different domains, their fusioning conforming to richer contextual information. This paper contributes in terms of ontology evolution with additional domains, context definitions, rules and inclusion of semantic queries. For the framework evaluation, multi-level cross-domain contexts collected from 20 users were used to ascertain abstract contexts, which served as basis for behavior modeling and lifestyle identification. The experimental results indicate a context recognition average accuracy of around 92.65% for the collected cross-domain contexts. PMID:29064459

A Strategy for Origins of Life Research.

PubMed

Scharf, Caleb; Virgo, Nathaniel; Cleaves, H James; Aono, Masashi; Aubert-Kato, Nathanael; Aydinoglu, Arsev; Barahona, Ana; Barge, Laura M; Benner, Steven A; Biehl, Martin; Brasser, Ramon; Butch, Christopher J; Chandru, Kuhan; Cronin, Leroy; Danielache, Sebastian; Fischer, Jakob; Hernlund, John; Hut, Piet; Ikegami, Takashi; Kimura, Jun; Kobayashi, Kensei; Mariscal, Carlos; McGlynn, Shawn; Menard, Brice; Packard, Norman; Pascal, Robert; Pereto, Juli; Rajamani, Sudha; Sinapayen, Lana; Smith, Eric; Switzer, Christopher; Takai, Ken; Tian, Feng; Ueno, Yuichiro; Voytek, Mary; Witkowski, Olaf; Yabuta, Hikaru

2015-12-01

Contents 1. Introduction 1.1. A workshop and this document 1.2. Framing origins of life science 1.2.1. What do we mean by the origins of life (OoL)? 1.2.2. Defining life 1.2.3. How should we characterize approaches to OoL science? 1.2.4. One path to life or many? 2. A Strategy for Origins of Life Research 2.1. Outcomes-key questions and investigations 2.1.1. Domain 1: Theory 2.1.2. Domain 2: Practice 2.1.3. Domain 3: Process 2.1.4. Domain 4: Future studies 2.2. EON Roadmap 2.3. Relationship to NASA Astrobiology Roadmap and Strategy documents and the European AstRoMap   Appendix I   Appendix II   Supplementary Materials  References.

Engineering and Application of Zinc Finger Proteins and TALEs for Biomedical Research.

PubMed

Kim, Moon-Soo; Kini, Anu Ganesh

2017-08-01

Engineered DNA-binding domains provide a powerful technology for numerous biomedical studies due to their ability to recognize specific DNA sequences. Zinc fingers (ZF) are one of the most common DNA-binding domains and have been extensively studied for a variety of applications, such as gene regulation, genome engineering and diagnostics. Another novel DNA-binding domain known as a transcriptional activator-like effector (TALE) has been more recently discovered, which has a previously undescribed DNA-binding mode. Due to their modular architecture and flexibility, TALEs have been rapidly developed into artificial gene targeting reagents. Here, we describe the methods used to design these DNA-binding proteins and their key applications in biomedical research.

Small vessel security strategy

DOT National Transportation Integrated Search

2008-04-01

This strategy identifies specific goals where efforts can achieve the greatest risk reduction across the breadth of the maritime domain. Its guiding principles are that: solutions shall be risk-based; education and training are the key tools for enha...

Application of oxime-diversification to optimize ligand interactions within a cryptic pocket of the polo-like kinase 1 polo-box domain | Center for Cancer Research

Cancer.gov

By a process involving initial screening of a set of 87 aldehydes using an oxime ligation-based strategy, we were able to achieve a several-fold affinity enhancement over one of the most potent previously known polo-like kinase 1 (Plk1) polo-box domain (PBD) binding inhibitors. This improved binding may result by accessing a newly identified auxiliary region proximal to a key

Atypical binding of the Swa2p UBA domain to ubiquitin.

PubMed

Matta-Camacho, Edna; Kozlov, Guennadi; Trempe, Jean-François; Gehring, Kalle

2009-02-20

Swa2p is an auxilin-like yeast protein that is involved in vesicular transport and required for uncoating of clathrin-coated vesicles. Swa2p contains a ubiquitin-associated (UBA) domain, which is present in a variety of proteins involved in ubiquitin (Ub)-mediated processes. We have determined a structural model of the Swa2p UBA domain in complex with Ub using NMR spectroscopy and molecular docking. Ub recognition occurs predominantly through an atypical interaction in which UBA helix alpha1 and the N-terminal part of helix alpha2 bind to Ub. Mutation of Ala148, a key residue in helix alpha1, to polar residues greatly reduced the affinity of the UBA domain for Ub and revealed a second low-affinity Ub-binding site located on the surface formed by helices alpha1 and alpha3. Surface plasmon resonance showed that the Swa2p UBA domain binds K48- and K63-linked di-Ub in a non-linkage-specific manner. These results reveal convergent evolution of a Ub-binding site on helix alpha1 of UBA domains involved in membrane protein trafficking.

The study of co-citation analysis and knowledge structure on healthcare domain

NASA Astrophysics Data System (ADS)

Chu, Kuo-Chung; Liu, Wen-I.; Tsai, Ming-Yu

2012-11-01

With the prevalence of Internet and digital archives, the online e-journal database facilitates scholars to search literature in a research domain, or to cross-search an inter-disciplined field; the key literature can be efficiently traced out. This study intends to build a Web-based citation analysis system, which consists of four modules, they are: 1) literature search module; (2) statistics module; (3) articles analysis module; and (4) co-citation analysis module. The system focuses on PubMed Central dataset that has 170,000 records. In a research domain, a specific keyword searches in terms of authors, journals, and core issues. In addition, we use data mining techniques for co-citation analysis. The results assist researchers with in-depth understanding of the domain knowledge. Having an automated system for co-citation analysis, it helps to understand changes, trends, and knowledge structure of research domain. For the best of our knowledge, the proposed system differentiates from existing online electronic retrieval database analysis function. Perhaps, the proposed system is going to be a value-added database of healthcare domain, and hope to contribute the researchers.

Perlecan domain V is neuroprotective and proangiogenic following ischemic stroke in rodents

PubMed Central

Lee, Boyeon; Clarke, Douglas; Al Ahmad, Abraham; Kahle, Michael; Parham, Christi; Auckland, Lisa; Shaw, Courtney; Fidanboylu, Mehmet; Orr, Anthony Wayne; Ogunshola, Omolara; Fertala, Andrzej; Thomas, Sarah A.; Bix, Gregory J.

2011-01-01

Stroke is the leading cause of long-term disability and the third leading cause of death in the United States. While most research thus far has focused on acute stroke treatment and neuroprotection, the exploitation of endogenous brain self-repair mechanisms may also yield therapeutic strategies. Here, we describe a distinct type of stroke treatment, the naturally occurring extracellular matrix fragment of perlecan, domain V, which we found had neuroprotective properties and enhanced post-stroke angiogenesis, a key component of brain repair, in rodent models of stroke. In both rat and mouse models, Western blot analysis revealed elevated levels of perlecan domain V. When systemically administered 24 hours after stroke, domain V was well tolerated, reached infarct and peri-infarct brain vasculature, and restored stroke-affected motor function to baseline pre-stroke levels in these multiple stroke models in both mice and rats. Post-stroke domain V administration increased VEGF levels via a mechanism involving brain endothelial cell α5β1 integrin, and the subsequent neuroprotective and angiogenic actions of domain V were in turn mediated via VEGFR. These results suggest that perlecan domain V represents a promising approach for stroke treatment. PMID:21747167

Frontal gamma noise power and cognitive domains in schizophrenia.

PubMed

Díez, Alvaro; Suazo, Vanessa; Casado, Pilar; Martín-Loeches, Manuel; Perea, María Victoria; Molina, Vicente

2014-01-30

The cognitive deficit profile is different among individuals with schizophrenia. We quantified the amount of electroencephalographic activity unlocked to stimuli onset (noise power) over frontal regions regarding deficit in cognitive domains. Forty-six patients with schizophrenia and 27 healthy controls underwent clinical, cognitive and electrophysiological assessments. Noise power studies may be considered complementary but not equivalent to induced power studies. We compared gamma and theta noise power magnitude during a P300 paradigm between subsets of patients divided according to cognitive deficit in key domains and controls. Patients displayed higher gamma noise power activity at Fz site and significantly lower performance in all cognitive domains when compared to controls. The subset of patients with cognitive deficit for working memory and problem solving/executive functions domains displayed significantly higher frontal-lateral noise power values in comparison to the subset of patients without cognitive deficit and controls. Patients with significant cognitive deficits in domains with greater frontal contribution are also characterized by an abnormally higher gamma band noise power over the frontal region. Our data may endorse various biological subsets within schizophrenia, characterized by the presence or absence of a significant cognitive deficit in frontal domains. © 2013 Published by Elsevier Ireland Ltd.

A domains-based taxonomy of supported accommodation for people with severe and persistent mental illness.

PubMed

Siskind, Dan; Harris, Meredith; Pirkis, Jane; Whiteford, Harvey

2013-06-01

A lack of definitional clarity in supported accommodation and the absence of a widely accepted system for classifying supported accommodation models creates barriers to service planning and evaluation. We undertook a systematic review of existing supported accommodation classification systems. Using a structured system for qualitative data analysis, we reviewed the stratification features in these classification systems, identified the key elements of supported accommodation and arranged them into domains and dimensions to create a new taxonomy. The existing classification systems were mapped onto the new taxonomy to verify the domains and dimensions. Existing classification systems used either a service-level characteristic or programmatic approach. We proposed a taxonomy based around four domains: duration of tenure; patient characteristics; housing characteristics; and service characteristics. All of the domains in the taxonomy were drawn from the existing classification structures; however, none of the existing classification structures covered all of the domains in the taxonomy. Existing classification systems are regionally based, limited in scope and lack flexibility. A domains-based taxonomy can allow more accurate description of supported accommodation services, aid in identifying the service elements likely to improve outcomes for specific patient populations, and assist in service planning.

The Role of Bacterial Enhancer Binding Proteins as Specialized Activators of σ54-Dependent Transcription

PubMed Central

2012-01-01

Summary: Bacterial enhancer binding proteins (bEBPs) are transcriptional activators that assemble as hexameric rings in their active forms and utilize ATP hydrolysis to remodel the conformation of RNA polymerase containing the alternative sigma factor σ54. We present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. The review is structured by introducing each of the three domains in turn: the central catalytic domain, the N-terminal regulatory domain, and the C-terminal DNA binding domain. The role of the central catalytic domain is presented with particular reference to (i) oligomerization, (ii) ATP hydrolysis, and (iii) the key GAFTGA motif that contacts σ54 for remodeling. Each of these functions forms a potential target of the signal-sensing N-terminal regulatory domain, which can act either positively or negatively to control the activation of σ54-dependent transcription. Finally, we focus on the DNA binding function of the C-terminal domain and the enhancer sites to which it binds. Particular attention is paid to the importance of σ54 to the bacterial cell and its unique role in regulating transcription. PMID:22933558

The Multi Domain Caldicellulosiruptor bescii CelA Cellulase Excels at the Hydrolysis of Crystalline Cellulose

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brunecky, Roman; Donohoe, Bryon S.; Yarbrough, John M.

The crystalline nature of cellulose microfibrils is one of the key factors influencing biomass recalcitrance which is a key technical and economic barrier to overcome to make cellulosic biofuels a commercial reality. To date, all known fungal enzymes tested have great difficulty degrading highly crystalline cellulosic substrates. We have demonstrated that the CelA cellulase from Caldicellulosiruptor bescii degrades highly crystalline cellulose as well as low crystallinity substrates making it the only known cellulase to function well on highly crystalline cellulose. Unlike the secretomes of cellulolytic fungi, which typically comprise multiple, single catalytic domain enzymes for biomass degradation, some bacterial systemsmore » employ an alternative strategy that utilizes multi-catalytic domain cellulases. Additionally, CelA is extremely thermostable and highly active at elevated temperatures, unlike commercial fungal cellulases. Furthermore we have determined that the factors negatively affecting digestion of lignocellulosic materials by C. bescii enzyme cocktails containing CelA appear to be significantly different from the performance barriers affecting fungal cellulases. Furthermore, we explore the activity and degradation mechanism of CelA on a variety of pretreated substrates to better understand how the different bulk components of biomass, such as xylan and lignin, impact its performance.« less

The Multi Domain Caldicellulosiruptor bescii CelA Cellulase Excels at the Hydrolysis of Crystalline Cellulose

DOE PAGES

Brunecky, Roman; Donohoe, Bryon S.; Yarbrough, John M.; ...

2017-08-29

The crystalline nature of cellulose microfibrils is one of the key factors influencing biomass recalcitrance which is a key technical and economic barrier to overcome to make cellulosic biofuels a commercial reality. To date, all known fungal enzymes tested have great difficulty degrading highly crystalline cellulosic substrates. We have demonstrated that the CelA cellulase from Caldicellulosiruptor bescii degrades highly crystalline cellulose as well as low crystallinity substrates making it the only known cellulase to function well on highly crystalline cellulose. Unlike the secretomes of cellulolytic fungi, which typically comprise multiple, single catalytic domain enzymes for biomass degradation, some bacterial systemsmore » employ an alternative strategy that utilizes multi-catalytic domain cellulases. Additionally, CelA is extremely thermostable and highly active at elevated temperatures, unlike commercial fungal cellulases. Furthermore we have determined that the factors negatively affecting digestion of lignocellulosic materials by C. bescii enzyme cocktails containing CelA appear to be significantly different from the performance barriers affecting fungal cellulases. Furthermore, we explore the activity and degradation mechanism of CelA on a variety of pretreated substrates to better understand how the different bulk components of biomass, such as xylan and lignin, impact its performance.« less

Crystal structure of the GTPase domain and the bundle signalling element of dynamin in the GDP state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anand, Roopsee; Eschenburg, Susanne; Reubold, Thomas F., E-mail: Reubold.Thomas@mh-hannover.de

Dynamin is the prototype of a family of large multi-domain GTPases. The 100 kDa protein is a key player in clathrin-mediated endocytosis, where it cleaves off vesicles from membranes using the energy from GTP hydrolysis. We have solved the high resolution crystal structure of a fusion protein of the GTPase domain and the bundle signalling element (BSE) of dynamin 1 liganded with GDP. The structure provides a hitherto missing snapshot of the GDP state of the hydrolytic cycle of dynamin and reveals how the switch I region moves away from the active site after GTP hydrolysis and release of inorganic phosphate.more » Comparing our structure of the GDP state with the known structures of the GTP state, the transition state and the nucleotide-free state of dynamin 1 we describe the structural changes through the hydrolytic cycle. - Highlights: • High resolution crystal structure of the GDP-state of a dynamin 1 GTPase-BSE fusion. • Visualizes one of the key states of the hydrolytic cycle of dynamin. • The dynamin-specific loop forms a helix as soon as a guanine base is present.« less

Traffic to the malaria parasite food vacuole: a novel pathway involving a phosphatidylinositol 3-phosphate-binding protein.

PubMed

McIntosh, Michael T; Vaid, Ankush; Hosgood, H Dean; Vijay, Justin; Bhattacharya, Anindita; Sahani, Mayurbhai H; Baevova, Pavlina; Joiner, Keith A; Sharma, Pushkar

2007-04-13

Phosphatidylinositol 3-phosphate (PI3P) is a key ligand for recruitment of endosomal regulatory proteins in higher eukaryotes. Subsets of these endosomal proteins possess a highly selective PI3P binding zinc finger motif belonging to the FYVE domain family. We have identified a single FYVE domain-containing protein in Plasmodium falciparum which we term FCP. Expression and mutagenesis studies demonstrate that key residues are involved in specific binding to PI3P. In contrast to FYVE proteins in other organisms, endogenous FCP localizes to a lysosomal compartment, the malaria parasite food vacuole (FV), rather than to cytoplasmic endocytic organelles. Transfections of deletion mutants further indicate that FCP is essential for trophozoite and FV maturation and that it traffics to the FV via a novel constitutive cytoplasmic to vacuole targeting pathway. This newly discovered pathway excludes the secretory pathway and is directed by a C-terminal 44-amino acid peptide domain. We conclude that an FYVE protein that might be expected to participate in vesicle targeting in the parasite cytosol instead has a vital and functional role in the malaria parasite FV.

Induced stem cell neoplasia in a cnidarian by ectopic expression of a POU domain transcription factor.

PubMed

Millane, R Cathriona; Kanska, Justyna; Duffy, David J; Seoighe, Cathal; Cunningham, Stephen; Plickert, Günter; Frank, Uri

2011-06-01

The evolutionary origin of stem cell pluripotency is an unresolved question. In mammals, pluripotency is limited to early embryos and is induced and maintained by a small number of key transcription factors, of which the POU domain protein Oct4 is considered central. Clonal invertebrates, by contrast, possess pluripotent stem cells throughout their life, but the molecular mechanisms that control their pluripotency are poorly defined. To address this problem, we analyzed the expression pattern and function of Polynem (Pln), a POU domain gene from the marine cnidarian Hydractinia echinata. We show that Pln is expressed in the embryo and adult stem cells of the animal and that ectopic expression in epithelial cells induces stem cell neoplasms and loss of epithelial tissue. Neoplasm cells downregulated the transgene but expressed the endogenous Pln gene and also Nanos, Vasa, Piwi and Myc, which are all known cnidarian stem cell markers. Retinoic acid treatment caused downregulation of Pln and the differentiation of neoplasm cells to neurosensory and epithelial cells. Pln downregulation by RNAi led to differentiation. Collectively, our results suggest an ancient role of POU proteins as key regulators of animal stem cells.

The structure of S . lividans acetoacetyl-CoA synthetase shows a novel interaction between the C-terminal extension and the N-terminal domain

DOE PAGES

Mitchell, Carter A.; Tucker, Alex C.; Escalante-Semerena, Jorge C.; ...

2014-12-09

The adenosine monoposphate-forming acyl-CoA synthetase enzymes catalyze a two-step reaction that involves the initial formation of an acyl adenylate that reacts in a second partial reaction to form a thioester between the acyl substrate and CoA. These enzymes utilize a Domain Alternation catalytic mechanism, whereby a ~110 residue C-terminal domain rotates by 140° to form distinct catalytic conformations for the two partial reactions. In this paper, the structure of an acetoacetyl-CoA synthetase (AacS) is presented that illustrates a novel aspect of this C-terminal domain. Specifically, several acetyl- and acetoacetyl-CoA synthetases contain a 30-residue extension on the C-terminus compared to othermore » members of this family. Finally, whereas residues from this extension are disordered in prior structures, the AacS structure shows that residues from this extension may interact with key catalytic residues from the N-terminal domain.« less

DNA Double-Strand Breaks Coupled with PARP1 and HNRNPA2B1 Binding Sites Flank Coordinately Expressed Domains in Human Chromosomes

PubMed Central

Fedoseeva, Daria M.; Sosin, Dmitri V.; Grachev, Sergei A.; Serebraykova, Marina V.; Romanenko, Svetlana A.; Vorobieva, Nadezhda V.; Kravatsky, Yuri V.

2013-01-01

Genome instability plays a key role in multiple biological processes and diseases, including cancer. Genome-wide mapping of DNA double-strand breaks (DSBs) is important for understanding both chromosomal architecture and specific chromosomal regions at DSBs. We developed a method for precise genome-wide mapping of blunt-ended DSBs in human chromosomes, and observed non-random fragmentation and DSB hot spots. These hot spots are scattered along chromosomes and delimit protected 50–250 kb DNA domains. We found that about 30% of the domains (denoted forum domains) possess coordinately expressed genes and that PARP1 and HNRNPA2B1 specifically bind DNA sequences at the forum domain termini. Thus, our data suggest a novel type of gene regulation: a coordinated transcription or silencing of gene clusters delimited by DSB hot spots as well as PARP1 and HNRNPa2B1 binding sites. PMID:23593027

The Scientific Competitiveness of Nations.

PubMed

Cimini, Giulio; Gabrielli, Andrea; Sylos Labini, Francesco

2014-01-01

We use citation data of scientific articles produced by individual nations in different scientific domains to determine the structure and efficiency of national research systems. We characterize the scientific fitness of each nation-that is, the competitiveness of its research system-and the complexity of each scientific domain by means of a non-linear iterative algorithm able to assess quantitatively the advantage of scientific diversification. We find that technological leading nations, beyond having the largest production of scientific papers and the largest number of citations, do not specialize in a few scientific domains. Rather, they diversify as much as possible their research system. On the other side, less developed nations are competitive only in scientific domains where also many other nations are present. Diversification thus represents the key element that correlates with scientific and technological competitiveness. A remarkable implication of this structure of the scientific competition is that the scientific domains playing the role of "markers" of national scientific competitiveness are those not necessarily of high technological requirements, but rather addressing the most "sophisticated" needs of the society.

Investigation of multilayer domains in large-scale CVD monolayer graphene by optical imaging

NASA Astrophysics Data System (ADS)

Yu, Yuanfang; Li, Zhenzhen; Wang, Wenhui; Guo, Xitao; Jiang, Jie; Nan, Haiyan; Ni, Zhenhua

2017-03-01

CVD graphene is a promising candidate for optoelectronic applications due to its high quality and high yield. However, multi-layer domains could inevitably form at the nucleation centers during the growth. Here, we propose an optical imaging technique to precisely identify the multilayer domains and also the ratio of their coverage in large-scale CVD monolayer graphene. We have also shown that the stacking disorder in twisted bilayer graphene as well as the impurities on the graphene surface could be distinguished by optical imaging. Finally, we investigated the effects of bilayer domains on the optical and electrical properties of CVD graphene, and found that the carrier mobility of CVD graphene is seriously limited by scattering from bilayer domains. Our results could be useful for guiding future optoelectronic applications of large-scale CVD graphene. Project supported by the National Natural Science Foundation of China (Nos. 61422503, 61376104), the Open Research Funds of Key Laboratory of MEMS of Ministry of Education (SEU, China), and the Fundamental Research Funds for the Central Universities.

Optical-domain subsampling for data efficient depth ranging in Fourier-domain optical coherence tomography

PubMed Central

Siddiqui, Meena; Vakoc, Benjamin J.

2012-01-01

Recent advances in optical coherence tomography (OCT) have led to higher-speed sources that support imaging over longer depth ranges. Limitations in the bandwidth of state-of-the-art acquisition electronics, however, prevent adoption of these advances into the clinical applications. Here, we introduce optical-domain subsampling as a method for imaging at high-speeds and over extended depth ranges but with a lower acquisition bandwidth than that required using conventional approaches. Optically subsampled laser sources utilize a discrete set of wavelengths to alias fringe signals along an extended depth range into a bandwidth limited frequency window. By detecting the complex fringe signals and under the assumption of a depth-constrained signal, optical-domain subsampling enables recovery of the depth-resolved scattering signal without overlapping artifacts from this bandwidth-limited window. We highlight key principles behind optical-domain subsampled imaging, and demonstrate this principle experimentally using a polygon-filter based swept-source laser that includes an intra-cavity Fabry-Perot (FP) etalon. PMID:23038343

Emergence of Huge Negative Spin-Transfer Torque in Atomically Thin Co layers

NASA Astrophysics Data System (ADS)

Je, Soong-Geun; Yoo, Sang-Cheol; Kim, Joo-Sung; Park, Yong-Keun; Park, Min-Ho; Moon, Joon; Min, Byoung-Chul; Choe, Sug-Bong

2017-04-01

Current-induced domain wall motion has drawn great attention in recent decades as the key operational principle of emerging magnetic memory devices. As the major driving force of the motion, the spin-orbit torque on chiral domain walls has been proposed and is currently extensively studied. However, we demonstrate here that there exists another driving force, which is larger than the spin-orbit torque in atomically thin Co films. Moreover, the direction of the present force is found to be the opposite of the prediction of the standard spin-transfer torque, resulting in the domain wall motion along the current direction. The symmetry of the force and its peculiar dependence on the domain wall structure suggest that the present force is, most likely, attributed to considerable enhancement of a negative nonadiabatic spin-transfer torque in ultranarrow domain walls. Careful measurements of the giant magnetoresistance manifest a negative spin polarization in the atomically thin Co films which might be responsible for the negative spin-transfer torque.

Thrombospondin Type-1 Repeat Domain-Containing Proteins Are Strongly Expressed in the Head Region of Hydra

PubMed Central

Hamaguchi-Hamada, Kayoko; Kurumata-Shigeto, Mami; Minobe, Sumiko; Fukuoka, Nozomi; Sato, Manami; Matsufuji, Miyuki; Koizumi, Osamu; Hamada, Shun

2016-01-01

The head region of Hydra, the hypostome, is a key body part for developmental control and the nervous system. We herein examined genes specifically expressed in the head region of Hydra oligactis using suppression subtractive hybridization (SSH) cloning. A total of 1414 subtracted clones were sequenced and found to be derived from at least 540 different genes by BLASTN analyses. Approximately 25% of the subtracted clones had sequences encoding thrombospondin type-1 repeat (TSR) domains, and were derived from 17 genes. We identified 11 TSR domain-containing genes among the top 36 genes that were the most frequently detected in our SSH library. Whole-mount in situ hybridization analyses confirmed that at least 13 out of 17 TSR domain-containing genes were expressed in the hypostome of Hydra oligactis. The prominent expression of TSR domain-containing genes suggests that these genes play significant roles in the hypostome of Hydra oligactis. PMID:27043211

δ-COP contains a helix C-terminal to its longin domain key to COPI dynamics and function

PubMed Central

Arakel, Eric C.; Richter, Kora P.; Clancy, Anne; Schwappach, Blanche

2016-01-01

Membrane recruitment of coatomer and formation of coat protein I (COPI)-coated vesicles is crucial to homeostasis in the early secretory pathway. The conformational dynamics of COPI during cargo capture and vesicle formation is incompletely understood. By scanning the length of δ-COP via functional complementation in yeast, we dissect the domains of the δ-COP subunit. We show that the μ-homology domain is dispensable for COPI function in the early secretory pathway, whereas the N-terminal longin domain is essential. We map a previously uncharacterized helix, C-terminal to the longin domain, that is specifically required for the retrieval of HDEL-bearing endoplasmic reticulum-luminal residents. It is positionally analogous to an unstructured linker that becomes helical and membrane-facing in the open form of the AP2 clathrin adaptor complex. Based on the amphipathic nature of the critical helix it may probe the membrane for lipid packing defects or mediate interaction with cargo and thus contribute to stabilizing membrane-associated coatomer. PMID:27298352

Domain Evolution and Functional Diversification of Sulfite Reductases

NASA Astrophysics Data System (ADS)

Dhillon, Ashita; Goswami, Sulip; Riley, Monica; Teske, Andreas; Sogin, Mitchell

2005-02-01

Sulfite reductases are key enzymes of assimilatory and dissimilatory sulfur metabolism, which occur in diverse bacterial and archaeal lineages. They share a highly conserved domain "C-X5-C-n-C-X3-C" for binding siroheme and iron-sulfur clusters that facilitate electron transfer to the substrate. For each sulfite reductase cluster, the siroheme-binding domain is positioned slightly differently at the N-terminus of dsrA and dsrB, while in the assimilatory proteins the siroheme domain is located at the C-terminus. Our sequence and phylogenetic analysis of the siroheme-binding domain shows that sulfite reductase sequences diverged from a common ancestor into four separate clusters (aSir, alSir, dsr, and asrC) that are biochemically distinct; each serves a different assimilatory or dissimilatory role in sulfur metabolism. The phylogenetic distribution and functional grouping in sulfite reductase clusters (dsrA and dsrB vs. aSiR, asrC, and alSir) suggest that their functional diversification during evolution may have preceded the bacterial/archaeal divergence.

Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaojing; Kuk, Jane; Moffat, Keith

2008-11-12

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 {angstrom} resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an 'arm' structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common andmore » may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.« less

Domain Name Server Security (DNSSEC) Protocol Deployment

DTIC Science & Technology

2014-10-01

all the time. For mobile devices, end-system validation is much more difficult due to the state of their networks, many of which do not allow...way to distribute keying information than the current public-key infrastructure (PKI) allows. In addition, it will take work to convince CDNs and...Control Protocol (TCP) or even DNS over Secure Sockets Layer (SSL). One of the important outcomes of our work is the realization that that a " mobile

Leveraging Embedded Training Systems to Build Higher Level Cognitive Skills in Warfighters

DTIC Science & Technology

2009-10-01

is not just passive, waiting for key information to be presented, but is an active process . The information that is available to military pilots...train situation awareness (SA) skills and knowledge in military settings. SA is the key cognitive construct upon which decision making rests and one...task analyses in the military domain settings that reveal the critical SA elements for a given warfighter role and the challenges they must contend

Functional evidence for the critical amino-terminal conserved domain and key amino acids of Arabidopsis 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE.

PubMed

Hsieh, Wei-Yu; Sung, Tzu-Ying; Wang, Hsin-Tzu; Hsieh, Ming-Hsiun

2014-09-01

The plant 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE (HDR) catalyzes the last step of the methylerythritol phosphate pathway to synthesize isopentenyl diphosphate and its allyl isomer dimethylallyl diphosphate, which are common precursors for the synthesis of plastid isoprenoids. The Arabidopsis (Arabidopsis thaliana) genomic HDR transgene-induced gene-silencing lines are albino, variegated, or pale green, confirming that HDR is essential for plants. We used Escherichia coli isoprenoid synthesis H (Protein Data Bank code 3F7T) as a template for homology modeling to identify key amino acids of Arabidopsis HDR. The predicted model reveals that cysteine (Cys)-122, Cys-213, and Cys-350 are involved in iron-sulfur cluster formation and that histidine (His)-152, His-241, glutamate (Glu)-242, Glu-243, threonine (Thr)-244, Thr-312, serine-379, and asparagine-381 are related to substrate binding or catalysis. Glu-242 and Thr-244 are conserved only in cyanobacteria, green algae, and land plants, whereas the other key amino acids are absolutely conserved from bacteria to plants. We used site-directed mutagenesis and complementation assay to confirm that these amino acids, except His-152 and His-241, were critical for Arabidopsis HDR function. Furthermore, the Arabidopsis HDR contains an extra amino-terminal domain following the transit peptide that is highly conserved from cyanobacteria, and green algae to land plants but not existing in the other bacteria. We demonstrated that the amino-terminal conserved domain was essential for Arabidopsis and cyanobacterial HDR function. Further analysis of conserved amino acids in the amino-terminal conserved domain revealed that the tyrosine-72 residue was critical for Arabidopsis HDR. These results suggest that the structure and reaction mechanism of HDR evolution have become specific for oxygen-evolving photosynthesis organisms and that HDR probably evolved independently in cyanobacteria versus other prokaryotes. © 2014 American Society of Plant Biologists. All Rights Reserved.

Monitoring and Evaluating the Transition of Large-Scale Programs in Global Health

PubMed Central

Bao, James; Rodriguez, Daniela C; Paina, Ligia; Ozawa, Sachiko; Bennett, Sara

2015-01-01

Purpose: Donors are increasingly interested in the transition and sustainability of global health programs as priorities shift and external funding declines. Systematic and high-quality monitoring and evaluation (M&E) of such processes is rare. We propose a framework and related guiding questions to systematize the M&E of global health program transitions. Methods: We conducted stakeholder interviews, searched the peer-reviewed and gray literature, gathered feedback from key informants, and reflected on author experiences to build a framework on M&E of transition and to develop guiding questions. Findings: The conceptual framework models transition as a process spanning pre-transition and transition itself and extending into sustained services and outcomes. Key transition domains include leadership, financing, programming, and service delivery, and relevant activities that drive the transition in these domains forward include sustaining a supportive policy environment, creating financial sustainability, developing local stakeholder capacity, communicating to all stakeholders, and aligning programs. Ideally transition monitoring would begin prior to transition processes being implemented and continue for some time after transition has been completed. As no set of indicators will be applicable across all types of health program transitions, we instead propose guiding questions and illustrative quantitative and qualitative indicators to be considered and adapted based on the transition domains identified as most important to the particular health program transition. The M&E of transition faces new and unique challenges, requiring measuring constructs to which evaluators may not be accustomed. Many domains hinge on measuring “intangibles” such as the management of relationships. Monitoring these constructs may require a compromise between rigorous data collection and the involvement of key stakeholders. Conclusion: Monitoring and evaluating transitions in global health programs can bring conceptual clarity to the transition process, provide a mechanism for accountability, facilitate engagement with local stakeholders, and inform the management of transition through learning. Further investment and stronger methodological work are needed. PMID:26681706

The linker connecting the two kringles plays a key role in prothrombin activation

PubMed Central

Pozzi, Nicola; Chen, Zhiwei; Pelc, Leslie A.; Shropshire, Daniel B.; Di Cera, Enrico

2014-01-01

The zymogen prothrombin is proteolytically converted by factor Xa to the active protease thrombin in a reaction that is accelerated >3,000-fold by cofactor Va. This physiologically important effect is paradigmatic of analogous cofactor-dependent reactions in the coagulation and complement cascades, but its structural determinants remain poorly understood. Prothrombin has three linkers connecting the N-terminal Gla domain to kringle-1 (Lnk1), the two kringles (Lnk2), and kringle-2 to the C-terminal protease domain (Lnk3). Recent developments indicate that the linkers, and particularly Lnk2, confer on the zymogen significant flexibility in solution and enable prothrombin to sample alternative conformations. The role of this flexibility in the context of prothrombin activation was tested with several deletions. Removal of Lnk2 in almost its entirety (ProTΔ146–167) drastically reduces the enhancement of thrombin generation by cofactor Va from >3,000-fold to 60-fold because of a significant increase in the rate of activation in the absence of cofactor. Deletion of Lnk2 mimics the action of cofactor Va and offers insights into how prothrombin is activated at the molecular level. The crystal structure of ProTΔ146–167 reveals a contorted architecture where the domains are not vertically stacked, kringle-1 comes within 9 Å of the protease domain, and the Gla-domain primed for membrane binding comes in contact with kringle-2. These findings broaden our molecular understanding of a key reaction of the blood coagulation cascade where cofactor Va enhances activation of prothrombin by factor Xa by compressing Lnk2 and morphing prothrombin into a conformation similar to the structure of ProTΔ146–167. PMID:24821807

Identification and analysis of mutational hotspots in oncogenes and tumour suppressors.

PubMed

Baeissa, Hanadi; Benstead-Hume, Graeme; Richardson, Christopher J; Pearl, Frances M G

2017-03-28

The key to interpreting the contribution of a disease-associated mutation in the development and progression of cancer is an understanding of the consequences of that mutation both on the function of the affected protein and on the pathways in which that protein is involved. Protein domains encapsulate function and position-specific domain based analysis of mutations have been shown to help elucidate their phenotypes. In this paper we examine the domain biases in oncogenes and tumour suppressors, and find that their domain compositions substantially differ. Using data from over 30 different cancers from whole-exome sequencing cancer genomic projects we mapped over one million mutations to their respective Pfam domains to identify which domains are enriched in any of three different classes of mutation; missense, indels or truncations. Next, we identified the mutational hotspots within domain families by mapping small mutations to equivalent positions in multiple sequence alignments of protein domainsWe find that gain of function mutations from oncogenes and loss of function mutations from tumour suppressors are normally found in different domain families and when observed in the same domain families, hotspot mutations are located at different positions within the multiple sequence alignment of the domain. By considering hotspots in tumour suppressors and oncogenes independently, we find that there are different specific positions within domain families that are particularly suited to accommodate either a loss or a gain of function mutation. The position is also dependent on the class of mutation.We find rare mutations co-located with well-known functional mutation hotspots, in members of homologous domain superfamilies, and we detect novel mutation hotspots in domain families previously unconnected with cancer. The results of this analysis can be accessed through the MOKCa database (http://strubiol.icr.ac.uk/extra/MOKCa).

The Dynamics and Evolutionary Potential of Domain Loss and Emergence

PubMed Central

Moore, Andrew D.; Bornberg-Bauer, Erich

2012-01-01

The wealth of available genomic data presents an unrivaled opportunity to study the molecular basis of evolution. Studies on gene family expansions and site-dependent analyses have already helped establish important insights into how proteins facilitate adaptation. However, efforts to conduct full-scale cross-genomic comparisons between species are challenged by both growing amounts of data and the inherent difficulty in accurately inferring homology between deeply rooted species. Proteins, in comparison, evolve by means of domain rearrangements, a process more amenable to study given the strength of profile-based homology inference and the lower rates with which rearrangements occur. However, adapting to a constantly changing environment can require molecular modulations beyond reach of rearrangement alone. Here, we explore rates and functional implications of novel domain emergence in contrast to domain gain and loss in 20 arthropod species of the pancrustacean clade. Emerging domains are more likely disordered in structure and spread more rapidly within their genomes than established domains. Furthermore, although domain turnover occurs at lower rates than gene family turnover, we find strong evidence that the emergence of novel domains is foremost associated with environmental adaptation such as abiotic stress response. The results presented here illustrate the simplicity with which domain-based analyses can unravel key players of nature's adaptational machinery, complementing the classical site-based analyses of adaptation. PMID:22016574

Size and mobility of lipid domains tuned by geometrical constraints

PubMed Central

Schütte, Ole M.; Mey, Ingo; Savić, Filip; Geil, Burkhard; Janshoff, Andreas

2017-01-01

In the plasma membrane of eukaryotic cells, proteins and lipids are organized in clusters, the latter ones often called lipid domains or “lipid rafts.” Recent findings highlight the dynamic nature of such domains and the key role of membrane geometry and spatial boundaries. In this study, we used porous substrates with different pore radii to address precisely the extent of the geometric constraint, permitting us to modulate and investigate the size and mobility of lipid domains in phase-separated continuous pore-spanning membranes (PSMs). Fluorescence video microscopy revealed two types of liquid-ordered (lo) domains in the freestanding parts of the PSMs: (i) immobile domains that were attached to the pore rims and (ii) mobile, round-shaped lo domains within the center of the PSMs. Analysis of the diffusion of the mobile lo domains by video microscopy and particle tracking showed that the domains’ mobility is slowed down by orders of magnitude compared with the unrestricted case. We attribute the reduced mobility to the geometric confinement of the PSM, because the drag force is increased substantially due to hydrodynamic effects generated by the presence of these boundaries. Our system can serve as an experimental test bed for diffusion of 2D objects in confined geometry. The impact of hydrodynamics on the mobility of enclosed lipid domains can have great implications for the formation and lateral transport of signaling platforms. PMID:28696315

Genomics-Based Security Protocols: From Plaintext to Cipherprotein

NASA Technical Reports Server (NTRS)

Shaw, Harry; Hussein, Sayed; Helgert, Hermann

2011-01-01

The evolving nature of the internet will require continual advances in authentication and confidentiality protocols. Nature provides some clues as to how this can be accomplished in a distributed manner through molecular biology. Cryptography and molecular biology share certain aspects and operations that allow for a set of unified principles to be applied to problems in either venue. A concept for developing security protocols that can be instantiated at the genomics level is presented. A DNA (Deoxyribonucleic acid) inspired hash code system is presented that utilizes concepts from molecular biology. It is a keyed-Hash Message Authentication Code (HMAC) capable of being used in secure mobile Ad hoc networks. It is targeted for applications without an available public key infrastructure. Mechanics of creating the HMAC are presented as well as a prototype HMAC protocol architecture. Security concepts related to the implementation differences between electronic domain security and genomics domain security are discussed.

Nature Contact and Human Health: A Research Agenda.

PubMed

Frumkin, Howard; Bratman, Gregory N; Breslow, Sara Jo; Cochran, Bobby; Kahn, Peter H; Lawler, Joshua J; Levin, Phillip S; Tandon, Pooja S; Varanasi, Usha; Wolf, Kathleen L; Wood, Spencer A

2017-07-31

At a time of increasing disconnectedness from nature, scientific interest in the potential health benefits of nature contact has grown. Research in recent decades has yielded substantial evidence, but large gaps remain in our understanding. We propose a research agenda on nature contact and health, identifying principal domains of research and key questions that, if answered, would provide the basis for evidence-based public health interventions. We identify research questions in seven domains: a ) mechanistic biomedical studies; b ) exposure science; c ) epidemiology of health benefits; d ) diversity and equity considerations; e ) technological nature; f ) economic and policy studies; and g ) implementation science. Nature contact may offer a range of human health benefits. Although much evidence is already available, much remains unknown. A robust research effort, guided by a focus on key unanswered questions, has the potential to yield high-impact, consequential public health insights. https://doi.org/10.1289/EHP1663.

Lateral polarity control of III-nitride thin film and application in GaN Schottky barrier diode

NASA Astrophysics Data System (ADS)

Li, Junmei; Guo, Wei; Sheikhi, Moheb; Li, Hongwei; Bo, Baoxue; Ye, Jichun

2018-05-01

N-polar and III-polar GaN and AlN epitaxial thin films grown side by side on single sapphire substrate was reported. Surface morphology, wet etching susceptibility and bi-axial strain conditions were investigated and the polarity control scheme was utilized in the fabrication of Schottky barrier diode where ohmic contact and Schottky contact were deposited on N-polar domains and Ga-polar domains, respectively. The influence of N-polarity on on-state resistivity and I–V characteristic was discussed, demonstrating that lateral polarity structure of GaN and AlN can be widely used in new designs of optoelectronic and electronic devices. Project partially supported by the National Key Research and Development Program of China (No. 2016YFB0400802), the National Natural Science Foundation of China (No. 61704176), and the Open project of Zhejiang Key Laboratory for Advanced Microelectronic Intelligent Systems and Applications (No. ZJUAMIS1704).

A conceptual framework for the domain of evidence-based design.

PubMed

Ulrich, Roger S; Berry, Leonard L; Quan, Xiaobo; Parish, Janet Turner

2010-01-01

The physical facilities in which healthcare services are performed play an important role in the healing process. Evidence-based design in healthcare is a developing field of study that holds great promise for benefiting key stakeholders: patients, families, physicians, and nurses, as well as other healthcare staff and organizations. In this paper, the authors present and discuss a conceptual framework intended to capture the current domain of evidence-based design in healthcare. In this framework, the built environment is represented by nine design variable categories: audio environment, visual environment, safety enhancement, wayfinding system, sustainability, patient room, family support spaces, staff support spaces, and physician support spaces. Furthermore, a series of matrices is presented that indicates knowledge gaps concerning the relationship between specific healthcare facility design variable categories and participant and organizational outcomes. From this analysis, the authors identify fertile research opportunities from the perspectives of key stakeholders.

Around and beyond 53BP1 Nuclear Bodies.

PubMed

Fernandez-Vidal, Anne; Vignard, Julien; Mirey, Gladys

2017-12-05

Within the nucleus, sub-nuclear domains define territories where specific functions occur. Nuclear bodies (NBs) are dynamic structures that concentrate nuclear factors and that can be observed microscopically. Recently, NBs containing the p53 binding protein 1 (53BP1), a key component of the DNA damage response, were defined. Interestingly, 53BP1 NBs are visualized during G1 phase, in daughter cells, while DNA damage was generated in mother cells and not properly processed. Unlike most NBs involved in transcriptional processes, replication has proven to be key for 53BP1 NBs, with replication stress leading to the formation of these large chromatin domains in daughter cells. In this review, we expose the composition and organization of 53BP1 NBs and focus on recent findings regarding their regulation and dynamics. We then concentrate on the importance of the replication stress, examine the relation of 53BP1 NBs with DNA damage and discuss their dysfunction.

Nature Contact and Human Health: A Research Agenda

PubMed Central

Bratman, Gregory N.; Breslow, Sara Jo; Cochran, Bobby; Kahn Jr, Peter H.; Lawler, Joshua J.; Levin, Phillip S.; Tandon, Pooja S.; Varanasi, Usha; Wolf, Kathleen L.; Wood, Spencer A.

2017-01-01

Background: At a time of increasing disconnectedness from nature, scientific interest in the potential health benefits of nature contact has grown. Research in recent decades has yielded substantial evidence, but large gaps remain in our understanding. Objectives: We propose a research agenda on nature contact and health, identifying principal domains of research and key questions that, if answered, would provide the basis for evidence-based public health interventions. Discussion: We identify research questions in seven domains: a) mechanistic biomedical studies; b) exposure science; c) epidemiology of health benefits; d) diversity and equity considerations; e) technological nature; f) economic and policy studies; and g) implementation science. Conclusions: Nature contact may offer a range of human health benefits. Although much evidence is already available, much remains unknown. A robust research effort, guided by a focus on key unanswered questions, has the potential to yield high-impact, consequential public health insights. https://doi.org/10.1289/EHP1663 PMID:28796634

Antitumor activity of novel chimeric peptides derived from cyclinD/CDK4 and the protein transduction domain 4.

PubMed

Wang, Haili; Chen, Xi; Chen, Yanping; Sun, Lei; Li, Guodong; Zhai, Mingxia; Zhai, Wenjie; Kang, Qiaozhen; Gao, Yanfeng; Qi, Yuanming

2013-02-01

CyclinD1/CDK4 and cyclinD3/CDK4 complexes are key regulators of the cell progression and therefore constitute promising targets for the design of anticancer agents. In the present study, the key peptide motifs were selected from these two complexes. Chimeric peptides with these peptides conjugated to the protein transduction domain 4 (PTD4) were designed and synthesized. The chimeric peptides, PTD4-D1, PTD4-D3, PTD4-K4 exhibited significant anti-proliferation effects on cancer cell lines. These peptides could compete with the cyclinD/CDK4 complex and induce the G1/S phase arrest and apoptosis of cancer cells. In the tumor challenge experiment, these peptides showed potent antitumor effects with no significant side effects. Our results suggested that these peptides could be served as novel leading compounds with potent antitumor activity.

Allostery Mediates Ligand Binding to WWOX Tumor Suppressor via a Conformational Switch

PubMed Central

Schuchardt, Brett J.; Mikles, David C.; Bhat, Vikas; McDonald, Caleb B.; Sudol, Marius; Farooq, Amjad

2014-01-01

While being devoid of the ability to recognize ligands itself, the WW2 domain is believed to aid ligand binding to WW1 domain in the context of WW1-WW2 tandem module of WWOX tumor suppressor. In an effort to test the generality of this hypothesis, we have undertaken here a detailed biophysical analysis of the binding of WW domains of WWOX alone and in the context of WW1-WW2 tandem module to an array of putative PPXY ligands. Our data show that while the WW1 domain of WWOX binds to all ligands in a physiologically-relevant manner, the WW2 domain does not. Moreover, ligand binding to WW1 domain in the context of WW1-WW2 tandem module is two-to-three-fold stronger than when treated alone. We also provide evidence that the WW domains within the WW1-WW2 tandem module physically associate so as to adopt a fixed spatial orientation relative to each other. Of particular note is the observation that the physical association of WW2 domain with WW1 blocks access to ligand. Consequently, ligand binding to WW1 domain not only results in the displacement of WW2 lid but also disrupts the physical association of WW domains in the liganded conformation. Taken together, our study underscores a key role of allosteric communication in the ability of WW2 orphan domain to chaperone physiological action of WW1 domain within the context of the WW1-WW2 tandem module of WWOX. PMID:25703206

OST-HTH: a novel predicted RNA-binding domain

PubMed Central

2010-01-01

Background The mechanism by which the arthropod Oskar and vertebrate TDRD5/TDRD7 proteins nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. Using sequence profile searches we identify a novel domain in these proteins that is widely conserved across eukaryotes and bacteria. Results Using contextual information from domain architectures, sequence-structure superpositions and available functional information we predict that this domain is likely to adopt the winged helix-turn-helix fold and bind RNA with a potential specificity for dsRNA. We show that in eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Conclusions Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized domain (DUF88). We present evidence that it is an RNAse belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains and might be recruited to degrade certain RNAs. Reviewers This article was reviewed by Sandor Pongor and Arcady Mushegian. PMID:20302647

What are the concerns and goals of women attending a urogynaecology clinic? Content analysis of free-text data from an electronic pelvic floor assessment questionnaire (ePAQ-PF).

PubMed

Gray, Thomas; Strickland, Scarlett; Pooranawattanakul, Sarita; Li, Weiguang; Campbell, Patrick; Jones, Georgina; Radley, Stephen

2018-06-27

Understanding patients' concerns and goals is essential for providing individualised care in urogynaecology. The study objectives were to undertake a content analysis of free-text concerns and goals recorded by patients using an electronic pelvic-floor questionnaire (ePAQ-PF) and measure how these related to self-reported symptom and health-related quality-of-life (HRQOL) data also recorded using ePAQ-PF. A total of 1996 consenting patients completed ePAQ-PF. Content analysis was undertaken of free-text responses to the item: 'Considering the issues that currently concern you the most, what do you hope to achieve from any help, advice or treatment?' Key content themes were identified by the lead researcher, and three researchers read and coded all recorded responses. Student's t test was used to compare ePAQ-PF domain scores for patients reporting concerns in the relevant domain with those who did not. In total, 63% of participants who completed the questionnaire, recorded at least one free-text item. Content analysis identified 1560 individual concerns coding into the 19 ePAQ-PF domains. Symptom scores were significantly higher for patients reporting free-text concerns in 18 domains (p < 0.05). Additional concerns relating specifically to body image were recorded by 11% of patients. Key areas of importance emerging for personal goals included cure/improvement, better understanding, incontinence pad use, sexual function and surgery. Free-text reporting in ePAQ-PF is utilised by patients and facilitates self-expression and discussion of issues impacting on HRQOL. The significant relationship between recorded free-text concerns and ePAQ-PF domain scores suggests convergent validity for the instrument. Development and psychometric testing of a domain to assess body image is proposed.

Factors in Patient Empowerment: A Survey of an Online Patient Research Network.

PubMed

Chiauzzi, Emil; DasMahapatra, Pronabesh; Cochin, Elisenda; Bunce, Mikele; Khoury, Raya; Dave, Purav

2016-12-01

Providers and healthcare organizations have begun recognizing the importance of patient empowerment as a driver of patient-centered care. Unfortunately, most studies have investigated empowerment with single diseases. Identifying factors of empowerment across conditions and populations would enable a greater understanding of this construct. The purpose of this study was to understand empowerment in relation to health information-seeking, interactions with providers and peers, and healthcare access in chronic disease patients. This study also sought to identify key empowerment factors and their association with patient characteristics. Participants were recruited through PatientsLikeMe, an online research platform where patients share their personal and medical history data. Patients completed an online survey that assessed self-reported health behavior (e.g. knowledge-seeking, experiences with healthcare providers, and peer interactions) and healthcare access. An exploratory factor analysis identified key empowerment domains. Domain level sum scores and sum of all domains (total score) were compared across patient characteristics and diseases. Overall, 3988 participants were included in the study, with the majority actively involved in their healthcare, but many cited difficulties with matching their treatment goals with those of their physician (34 %) and spending sufficient time with the physician (36 %). Factor analysis identified two domains-Positive Patient-Provider Interaction, and Knowledge and Personal Control-that explained >60 % of the overall variance in the observed variables. Mean total empowerment scores for patients with a primary complaint of Parkinson's disease (61.8) and multiple sclerosis (60.3) were significantly greater than fibromyalgia (55.3) and chronic fatigue syndrome (54.8). Patients who were older, male, more educated, and insured also reported significantly greater levels of empowerment. The two domains of empowerment identified in this study are consistent with previous studies, but the differences in empowerment levels across diseases suggest a need for further studies on disease-related attributes of empowerment. Future research should examine the pathways for empowerment, as well as the relationship between empowerment domains and clinical outcomes.

Semantic Interoperability Almost Without Using The Same Vocabulary: Is It Possible?

NASA Astrophysics Data System (ADS)

Krisnadhi, A. A.

2016-12-01

Semantic interoperability, which is a key requirement in realizing cross-repository data integration, is often understood as using the same ontology or vocabulary. Consequently, within a particular domain, one can easily assume that there has to be one unifying domain ontology covering as many vocabulary terms in the domain as possible in order to realize any form of data integration across multiple data sources. Furthermore, the desire to provide very precise definition of those many terms led to the development of huge, foundational and domain ontologies that are comprehensive, but too complicated, restrictive, monolithic, and difficult to use and reuse, which cause common data providers to avoid using them. This problem is especially true in a domain as diverse as geosciences as it is virtually impossible to reach an agreement to the semantics of many terms (e.g., there are hundreds of definitions of forest used throughout the world). To overcome this challenge, modular ontology architecture has emerged in recent years, fueled among others, by advances in the ontology design pattern research. Each ontology pattern models only one key notion. It can act as a small module of a larger ontology. Such a module is developed in such a way that it is largely independent of how other notions in the same domain are modeled. This leads to an increased reusability. Furthermore, an ontology formed out of such modules would have an improved understandability over large, monolithic ontologies. Semantic interoperability in the aforementioned architecture is not achieved by enforcing the use of the same vocabulary, but rather, promoting alignment to the same ontology patterns. In this work, we elaborate how this architecture realizes the above idea. In particular, we describe how multiple data sources with differing perspectives and vocabularies can interoperate through this architecture. Building the solution upon semantic technologies such as Linked Data and the Web Ontology Language (OWL), we demonstrate how a data integration solution based on this idea can be realized over different data repositories.

Structure of the BTB Domain of Keap1 and Its Interaction with the Triterpenoid Antagonist CDDO

PubMed Central

Cleasby, Anne; Yon, Jeff; Day, Philip J.; Richardson, Caroline; Tickle, Ian J.; Williams, Pamela A.; Callahan, James F.; Carr, Robin; Concha, Nestor; Kerns, Jeffrey K.; Qi, Hongwei; Sweitzer, Thomas; Ward, Paris; Davies, Thomas G.

2014-01-01

The protein Keap1 is central to the regulation of the Nrf2-mediated cytoprotective response, and is increasingly recognized as an important target for therapeutic intervention in a range of diseases involving excessive oxidative stress and inflammation. The BTB domain of Keap1 plays key roles in sensing environmental electrophiles and in mediating interactions with the Cul3/Rbx1 E3 ubiquitin ligase system, and is believed to be the target for several small molecule covalent activators of the Nrf2 pathway. However, despite structural information being available for several BTB domains from related proteins, there have been no reported crystal structures of Keap1 BTB, and this has precluded a detailed understanding of its mechanism of action and interaction with antagonists. We report here the first structure of the BTB domain of Keap1, which is thought to contain the key cysteine residue responsible for interaction with electrophiles, as well as structures of the covalent complex with the antagonist CDDO/bardoxolone, and of the constitutively inactive C151W BTB mutant. In addition to providing the first structural confirmation of antagonist binding to Keap1 BTB, we also present biochemical evidence that adduction of Cys 151 by CDDO is capable of inhibiting the binding of Cul3 to Keap1, and discuss how this class of compound might exert Nrf2 activation through disruption of the BTB-Cul3 interface. PMID:24896564

Clinical Research Informatics: Challenges, Opportunities and Definition for an Emerging Domain

PubMed Central

Embi, Peter J.; Payne, Philip R.O.

2009-01-01

Objectives Clinical Research Informatics, an emerging sub-domain of Biomedical Informatics, is currently not well defined. A formal description of CRI including major challenges and opportunities is needed to direct progress in the field. Design Given the early stage of CRI knowledge and activity, we engaged in a series of qualitative studies with key stakeholders and opinion leaders to determine the range of challenges and opportunities facing CRI. These phases employed complimentary methods to triangulate upon our findings. Measurements Study phases included: 1) a group interview with key stakeholders, 2) an email follow-up survey with a larger group of self-identified CRI professionals, and 3) validation of our results via electronic peer-debriefing and member-checking with a group of CRI-related opinion leaders. Data were collected, transcribed, and organized for formal, independent content analyses by experienced qualitative investigators, followed by an iterative process to identify emergent categorizations and thematic descriptions of the data. Results We identified a range of challenges and opportunities facing the CRI domain. These included 13 distinct themes spanning academic, practical, and organizational aspects of CRI. These findings also informed the development of a formal definition of CRI and supported further representations that illustrate areas of emphasis critical to advancing the domain. Conclusions CRI has emerged as a distinct discipline that faces multiple challenges and opportunities. The findings presented summarize those challenges and opportunities and provide a framework that should help inform next steps to advance this important new discipline. PMID:19261934

Education, implementation, and policy barriers to greater integration of palliative care: A literature review.

PubMed

Aldridge, Melissa D; Hasselaar, Jeroen; Garralda, Eduardo; van der Eerden, Marlieke; Stevenson, David; McKendrick, Karen; Centeno, Carlos; Meier, Diane E

2016-03-01

Early integration of palliative care into the management of patients with serious disease has the potential to both improve quality of life of patients and families and reduce healthcare costs. Despite these benefits, significant barriers exist in the United States to the early integration of palliative care in the disease trajectory of individuals with serious illness. To provide an overview of the barriers to more widespread palliative care integration in the United States. A literature review using PubMed from 2005 to March 2015 augmented by primary data collected from 405 hospitals included in the Center to Advance Palliative Care's National Palliative Care Registry for years 2012 and 2013. We use the World Health Organization's Public Health Strategy for Palliative Care as a framework for analyzing barriers to palliative care integration. We identified key barriers to palliative care integration across three World Health Organization domains: (1) education domain: lack of adequate education/training and perception of palliative care as end-of-life care; (2) implementation domain: inadequate size of palliative medicine-trained workforce, challenge of identifying patients appropriate for palliative care referral, and need for culture change across settings; (3) policy domain: fragmented healthcare system, need for greater funding for research, lack of adequate reimbursement for palliative care, and regulatory barriers. We describe the key policy and educational opportunities in the United States to address and potentially overcome the barriers to greater integration of palliative care into the healthcare of Americans with serious illness. © The Author(s) 2015.

Addictions Neuroclinical Assessment: A Neuroscience-Based Framework for Addictive Disorders.

PubMed

Kwako, Laura E; Momenan, Reza; Litten, Raye Z; Koob, George F; Goldman, David

2016-08-01

This article proposes a heuristic framework for the Addictions Neuroclinical Assessment that incorporates key functional domains derived from the neurocircuitry of addiction. We review how addictive disorders (ADs) are presently diagnosed and the need for new neuroclinical measures to differentiate patients who meet clinical criteria for addiction to the same agent while differing in etiology, prognosis, and treatment response. The need for a better understanding of the mechanisms provoking and maintaining addiction, as evidenced by the limitations of current treatments and within-diagnosis clinical heterogeneity, is articulated. In addition, recent changes in the nosology of ADs, challenges to current classification systems, and prior attempts to subtype individuals with ADs are described. Complementary initiatives, including the Research Domain Criteria project, that have established frameworks for the neuroscience of psychiatric disorders are discussed. Three domains-executive function, incentive salience, and negative emotionality-tied to different phases in the cycle of addiction form the core functional elements of ADs. Measurement of these domains in epidemiologic, genetic, clinical, and treatment studies will provide the underpinnings for an understanding of cross-population and temporal variation in addictions, shared mechanisms in addictive disorders, impact of changing environmental influences, and gene identification. Finally, we show that it is practical to implement such a deep neuroclinical assessment using a combination of neuroimaging and performance measures. Neuroclinical assessment is key to reconceptualizing the nosology of ADs on the basis of process and etiology, an advance that can lead to improved prevention and treatment. Published by Elsevier Inc.

Structural basis of nSH2 regulation and lipid binding in PI3Kα.

PubMed

Miller, Michelle S; Schmidt-Kittler, Oleg; Bolduc, David M; Brower, Evan T; Chaves-Moreira, Daniele; Allaire, Marc; Kinzler, Kenneth W; Jennings, Ian G; Thompson, Philip E; Cole, Philip A; Amzel, L Mario; Vogelstein, Bert; Gabelli, Sandra B

2014-07-30

We report two crystal structures of the wild-type phosphatidylinositol 3-kinase α (PI3Kα) heterodimer refined to 2.9 Å and 3.4 Å resolution: the first as the free enzyme, the second in complex with the lipid substrate, diC4-PIP₂, respectively. The first structure shows key interactions of the N-terminal SH2 domain (nSH2) and iSH2 with the activation loop that suggest a mechanism by which the enzyme is inhibited in its basal state. In the second structure, the lipid substrate binds in a positively charged pocket adjacent to the ATP-binding site, bordered by the P-loop, the activation loop and the iSH2 domain. An additional lipid-binding site was identified at the interface of the ABD, iSH2 and kinase domains. The ability of PI3Kα to bind an additional PIP₂ molecule was confirmed in vitro by fluorescence quenching experiments. The crystal structures reveal key differences in the way the nSH2 domain interacts with wild-type p110α and with the oncogenic mutant p110αH1047R. Increased buried surface area and two unique salt-bridges observed only in the wild-type structure suggest tighter inhibition in the wild-type PI3Kα than in the oncogenic mutant. These differences may be partially responsible for the increased basal lipid kinase activity and increased membrane binding of the oncogenic mutant.